Method for the treatment of a sample containing biomolecules

ABSTRACT

The invention generally provides a method for the sample preparation for a subsequent preparation, processing or analysis method of a sample containing an at least one species of nucleic acid and/or one species of protein, whereby the method comprises the following steps: A) providing a sample which contains at least one species of a nucleic acid and/or of a protein, B) contacting the sample with a fluid or solid composition to produce a fluid sample preparation, whereby the composition contains at least a nitrogenous compound, which is selected from the group consisting of a) polyamines, b) amino acids, and oligo- and polypeptides, c) nitrogenous heterocyclic compounds, including homo- oder heteropolymers, which comprise these nitrogenous compounds, d) amines of the type R 1 R 2 NR 3 , whereby R 1 , R 2  and R 3  are chosen independently from one another from the group consisting of H, C 1 -C 5 -alkyl groups and aryl groups, whereby R 1 , R 2  and R 3  are not H simultaneously, e) carboxylic acid amides, f) inorganic ammonium salts, g) ammonium groups containing inner salt compounds, h) antibiotica binding nucleic acid, i) compounds which bind in the small cavity of the DNA, and mixtures of two or more of these compounds. The invention provides in particular a method for the lysis of a biological sample, and methods for the stabilization of biomolecules, a method for the decrease of inhibiting effects in a sample containing biomolecules and a differential masking method.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a divisional application of U.S. application Ser. No. 11/910,247filed Dec. 31, 2007, now U.S. Pat. No. 7,838,233 which is a §371National Stage Application of International Application No.PCT/EP2006/002961 filed Apr. 1, 2006, which claims priority from GermanApplication No. 10 2005 015 005.5 filed Apr. 1, 2005.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a method for the treatment of a samplecontaining biomolecules. The invention further relates to a method forthe lysis of a biological sample, a method for the stabilisation ofnucleic acids and/or proteins, a method for the reduction of inhibitingeffects in a sample containing nucleic acids and/or proteins, a methodfor the differential masking of nucleic acids and analysis methods whichbuild on the previous methods or incorporate them.

2. Description of Related Art

It has been known for a long time that the genetic origin and thefunctional activity of a cell can be determined and examined by studiesof biomolecules as e.g. its nucleic acids or proteins. The analyses ofthese molecules enable the direct access to the origin of the activitiesof cells. They are thereby potentially superior to indirect conventionalmethods as e.g. the detection of metabolites. This has led to a widedistribution of nucleic acid and protein analyses in previous years. Thebiomolecular analyses are thus already used in many areas, e.g. inmedical and clinical diagnostics, in pharmaceutics in the developmentand evaluation of drugs, in food analysis and during the supervision offood production, in agriculture during the breeding of agricultural cropand farm animals and in the environment analysis and in many researchareas.

The activities of genes can for example be determined directly by theanalysis of the RNA, in particular the mRNA in cells. The quantitativeanalysis of transcript samples (mRNA samples) in cells by modernmolecular-biological methods as e.g. real-time reverse transcriptase PCR(“Real-Time RT-PCR”) or gene expression chip analyses enables e.g. therecognition of wrongly expressed genes whereby e.g. metabolic disorders,infections or the formation of cancer can be recognised. The analysis ofthe DNA, e.g. from cells, by molecular biological methods as e.g. PCR,RFLP, AFLP or sequencing enables e.g. the proof of genetic defects orthe determination of the HLA-type and other genetic markers.

The analysis of genomic DNA and RNA is also used for the directdetection of infectious agents, such as viruses, bacteria etc.

It is the condition for all analysis methods of biomolecules frombiological samples that these biomolecules as e.g. DNA, RNA or proteinsare made accessible for the corresponding analysis method. Contents ofcells or organisms can usually only be analysed when the contents arepresent in the analysis medium, that is, are e.g. transferred from thecell or the organism into the analysis medium. The cells/organisms aredisintegrated for this purpose, so that the contents are not presentwithin but outside of the organism or the cells and the contents of theorganism or the cell are freely accessible for the analysis. Thedisintegration of organisms or parts of organisms (e.g. cells) is alsocalled lysis, the disintegrated organisms are also called lysates.

The disintegration of samples, e.g. organisms, should take place ascompletely as possible on two counts: (1) All areas of the sample, e.g.of the organism should be disintegrated, so that the contents ofpossibly all parts of an organism are released in the sample. (2) Thedisintegration of the sample, e.g. of the organisms, is only completedwhen the contents were made accessible for the analysis. While theorganisms were disintegrated, but the contents still covered, e.g. bycell compartments, an analysis of the contents cannot be carried out ina quantitative manner.

Presently, several lysis methods are known. A cleaning of the contentsto be analysed is followed in the most lysis methods, so as to free thecontents from all materials which counteract an analysis. Some examplesare to be described in the following:

Lysis with detergents: Detergents are amphipatic molecules whichdissolve the hydrophobic membrane of cells so that the contents of thecells outpour into the environment. E.g., non-ionic and ionic detergentsbelong to these. The detergents triton-X100, Nonidet-P40, sodiumdodecylsulfate (sodiumdodecyl sulfate, SDS), or also cationic detergents ase.g. N-cetyl-N,N,N-trimethyl-ammonium bromide (CTAB) amongst others havefurther use for the disintegration of organisms. Many methods withcationic detergents were described and patented for the lysis oforganisms and for the isolation of nucleic acids (NA). Nucleic acids cane.g. be complexed by cationic detergents for their protection andcleaning. The methods described in the following US patents and USpatent applications are part of these methods: U.S. Pat. No. 6,602,718,U.S. Pat. No. 6,617,170, U.S. Pat. No. 5,010,183, U.S. Pat. No.5,985,572, U.S. Pat. No. 5,300,635, U.S. Pat. No. 5,728,822, and US2002/0146677 A1, US 2004/0048384 A1, US 2004/0115689 A1, US 2004/0014703A1. The lysis method with ammonium salts as e.g.N-cetyl-N,N,N-trimethyl-ammonium bromide (CTAB) use amphipatic ammoniumsalts which contain a longer hydrocarbon chain of at least 6 C atoms.

B) Lysis with water: During the lysis with water, the properties ofsemipermeable membranes of cells are used which envelope these. Thesemembranes are water-permeable, but not for salts or larger molecules. Ifa cell with its contents of salt and other larger molecules istransferred into a fluid, which contains a lower salt concentration thanthe cell interior, the cell will absorb water until the saltconcentration within and outside the cell is balanced. If theconcentration difference between the cell interior and the outer fluidis sufficiently large, the cell will absorb water until it bursts.

C) Lysis with organic solvents: the hydrophobic membranes of cells canbe destroyed by organic solvent. The lipids of the membranes and thelipophilic protein components of the membranes are hereby absorbed inthe organic phase. The cell contents remain mostly in the hydrophilicphase or at the boundary layer between the lipophilic and thehydrophilic phase. Phenol is often used with this type of lysis.

D) Lysis with chaotropic salts: chaotropic salts destroy the structureof water based on the formation of hydrogen bridge bonds, so that thedouble layer structure of membranes cannot be maintained anymore. Thesemembranes are thereby dissolved and the lysis takes place, whereby thecell contents pour into the chaotropic environment. This method is usedwith a number of methods for isolating nucleic acids and proteins, e.g.in the commercially available RNeasy®-, QIAamp®-methods or thedenaturating disintegration of cells for protein cleaning.

It is desirable for the following cleaning steps or detection reactionswhich are carried out with the obtained lysate that the relevantcontents of the cell are transferred as completely as possible into thelysate, as the amount which is necessary for the detection or for theisolation of a given amount of a biomolecule such as DNA or RNA, can bereduced further.

With the quantitative and the qualitative analysis of biomolecules ase.g. nucleic acids and proteins, the preservation of their integrity isof great importance. In particular nucleic acid such as DNA and, to ahigher extent, RNA are subject to different influences after the removalof the biological samples from their natural environment, which can leadto a change or degradation of the DNA or RNA. For example, the enzymaticdegradation of these nucleic acids or the degradation of DNA under theinfluence of shear forces occurring in the sample during the lysis arementioned.

It is known that the preservation of the integrity of nucleic acids andproteins can be achieved by (A) cleaning of the NA or proteins, (B)dehydration, (C) protection against degrading enzymes or (D) complexing.This is described shortly in the following:

Cleaning of the nucleic acids or proteins: during the cleaning, nucleicacids or proteins are freed from all substances or molecules which arecontained in the biological sample and which can damage the integrity ofthe nucleic acids or the proteins permanently. These cleaning methodsare e.g. affinity chromatography, protein salting out methods, cleaningof nucleic acids or proteins at solid phases. The solid phase can e.g.be an ion exchanger as is described in U.S. Pat. Nos. 5,990,301, and6,020,186 for example. Alternatively, the use of porous matrices isdescribed, e.g. in U.S. Pat. No. 6,180,778 or U.S. Pat. No. 5,496,562.

(B) Dehydration: a dehydration of the nucleic acid or proteins causesthat damaging processes, which can take place when the sample with thenucleic acids or proteins are dissolved in water, are blocked orprevented. These damaging processes are e.g. the enzymatic degradationby proteases or nucleases. Thus, the isolated nucleic acid can bedehydrated e.g. by precipitation (precipitation) by means of salt andalcohol (Current protocols in molecular biology, e.g. p. 1.6.1. AlkalineLysis Miniprep). Nucleic acids can also be protected from degradation inbiological samples as e.g. in tissue parts or microscopic sections bydehydration. This is described in the description U.S. Pat. No.6,528,641 for example. The reagents are infiltrated into the intactsample in the method described there, whereby not only a dehydration,but also a precipitation of proteins as e.g. nucleases is effected,which are then present in the dehydrated sample in an inactive manner.The use of ammonium sulfate as dehydrating agent is particularlydescribed there. A precipitation of DNA is also effected in the cleaningof DNA described in the patent application US 2002/0197637, wherebypolyamines are used for cleaning and the polyamines lead to acondensation of the DNA, whereby a damage of the DNA by shearing shallbe avoided with mechanical disintegration.

(C) Protection from degrading enzymes: it has been known for a long timethat proteases and nucleases (enzymes disintegrating nucleic acid) canbe specifically inhibited. Thus, the DNase I can be inhibited by e.g.Mg²⁺- or Ca²⁺-complexing agents. RNases can be inhibited e.g. byspecific RNase inhibitors or by reducing agents. These inhibitors aredescribed in the U.S. Pat. Nos. 5,552,302 and 6,777,210.

(D) Complexing: Another variant of the cleaning provides a complexationwith quaternay ammonium salts forming micelles for the protection of thenucleic acids. The complexing of the nucleic acids thus leads to theprotection from nucleases. Quaternary ammonium salts are used thereby,which function as cationic detergents and form micelles. For this it isnecessary that the quaternary ammonium salt has at least one long-chaincarbon chain as substituent. The U.S. Pat. Nos. 6,602,718, 6,617,170,5,010,183, 5,985,572, 5,300,635, 5,728,822 and the US patentapplications US 2002/0146677A1, US 2004/0048384A1, US 2004/0115689, andUS 2004/0014703A1 are counted amongst these or similar methods.

U.S. Pat. No. 6,821,752 describes a cleaning and extraction of proteinsin the presence of amphipatic amines, that is, of compounds acting asdetergents in a similar manner.

The compounds provided for the separation or complexation of the nucleicacids or proteins is restricted in that they should behave as inert aspossible with regard to the isolation method or analysis method carriedout subsequently, that is, should not influence the subsequent isolationor analysis in a disadvantageous manner. Otherwise, they have to bedecomplexed in a further reconditioning step.

The above state of the art shows that sufficient stabilisation ofnucleic acids and proteins from biological samples usually requiresadditional reconditioning steps by which the sample is split. Methodsfor the stabilisation which make these additional reconditioning stepsunnecessary and which use stabilising reagents which can be used asversatile as possible, are therefore advantageous.

A further problem which can occur with the analysis of biomolecules suchas nucleic acids or samples containing proteins, is the fact thatbiomolecules of a first type can be impaired by biomolecules of a secondtype in such a sample. Sometimes, biomolecules of the second types shallalso be analysed, whereby biomolecules of the first or another type willthen act in a disrupting manner during the analysis. An example amongstmany is mentioned here to clarify this: A sample contains cells of acertain organism. A detection of a nucleic acid of these cells by anoligonucleotide in the presence of proteins binding nucleic acid can forexample be influenced in a disadvantageous manner. Assuming that acertain species of DNA is to be detected in the present example, theproteins binding the DNA represent an inhibiting substance. In anotherexample, e.g. the analysis of proteins binding DNA, a DNA which can bindto the proteins binding DNA can have a disadvantageous influence on theresult of the analysis, as the nucleic acid acts as inhibiting substancein this case and leads to a falsification of the results of theanalysis.

Usual methods for excluding these disadvantageous interactions betweendifferent biomolecules provide to separate the biomolecules which areinfluencing each other to avoid disturbances. These methods thus oftenprovide a cleaning step, in which certain species of biomolecules areremoved from a sample. The concentration of the biomolecules amongstthemselves is thereby changed by the separation method, so that thedesired biomolecules are enriched, but the other ones are reduced intheir concentrations.

Known methods for the separation of biomolecules include the followingmethods:

Separation of biomolecules by salting out methods: Salting out methodsare used to separate parts of the biological sample which can beprecipitated by a certain amount of salts from the sample. These methodscan be used on the one hand to precipitate the part to be cleaned withsalt. The ammonium sulfate precipitation of proteins represents such aknown method. On the other hand, this method can also be used in thereverse direction, an that the material to be cleaned is freed from aplurality of contaminating molecules, but is not precipitated itself. Anexample for this is the protein precipitation by potassium acetateduring the isolation of DNA.

Separation of biomolecules by chromatography: Biomolecules can, due totheir properties, be cleaned and separated by several chromatographymethods. These properties can concern their size, their charge, theirhydrophobity or their affinity to certain surfaces or haptenes, tomention only a few possibilities. Chromatography is to be explained herewith the example of the ion exchange chromatography: There are twopossibilities for a series of chemical biomolecules to be cleaned by ionexchange chromatography. The biomolecule to be isolated can on the onehand be bound to the ion exchange chromatography material, whereas thecontaminating substances are not bound and can be separated from thebiomolecule to be isolated in this manner (e.g. anion exchangechromatography for the cleaning of negatively charged nucleic acids). Onthe other hand, contaminating substances can also be bound to thechromatography material, and the biomolecule to be isolated can then becaught in the break-through or in the washing buffer (e.g. cationexchange chromatography for the cleaning of the negatively chargednucleic acids). Examples of such a method are described in U.S. Pat. No.5,990,301 and WO0248164.

(C) Separation of biomolecules at solid surfaces: A number of surfaceshave the property to be able to bind certain biomolecules in a definedbinding environment. Theses binding properties can be used for thecleaning of biomolecules. This will be explained here with the exampleof the cleaning of nucleic acid at silica surfaces. Silica surfaces, beit microparticles or membranes, can bind nucleic acids in the presenceof chaotropic salts having a high concentration. But other molecules ase.g. proteins do not bind to these surfaces and are thus separated. Thenucleic acid can be obtained in a pure form after the washing of thesilica surface. Examples for this are described in the U.S. Pat. Nos.5,990,301, 6,020,186 and 6,180,778.

(D) Separation of biomolecules by selective complexing: Some separationmethods complex biomolecules selectively, so that these can be separatedfrom the other contents of the sample by a centrifugation step or by afiltration step. Examples for this are described in U.S. Pat. Nos.5,728,822 and 5,985,572.

The use of ammonium sulfate for the neutralisation of inhibiting effectsat samples containing RNA is described in the US patent application US2002/0115851. These samples contain purified amounts of RNA. However, itis described in the literature that inorganic ammonium salts as e.g.ammonium sulfate have the disadvantage that certain partial activitiesof polymerases (e.g. 3′-5′ exonuclease activity) can be changed and thepresence of ammonium sulfate can thereby have a disadvantageous effecton the polymerase reactions carried out for the subsequent analysis(Tsurumi et al. “Functional Expression and Characterization of theEpstein-Barr Virus DNA Polymerase Catalytic Subunit”, Journal ofVirology, Vol 67, No. 8, 1993, p. 4651-4658)

The described methods require a preceding separation of the biomoleculesaffecting the detection reaction in a disadvantageous manner from thesample or presume these. Consequently, a need exists for a simplifiedmethod with which the inhibiting effect of certain biomolecules insamples can be removed in such a measure that a reliable detectionreaction can be carried out with the sample.

A further problem which often occurs during the separation of nucleicacids, is founded in the fact that ribonucleic acid (RNA) anddeoxyribonucleic acid (DNA) represent biomolecules which are verysimilar in their chemical properties. Thus, there is often thedifficulty to separate these from each other. For a plurality ofapplications, it is nevertheless of utmost importance to produceDNA-free RNA or RNA-free DNA: contaminating genomic DNA in RNApreparations can for example lead to quantitatively wrong results inRT-PCR experiments.

At present, a number of methods exist which make it possible to enrichRNA or DNA differentially. Different methods can be distinguished inprincipal:

On the one hand, enzymes can be used which specifically degrade DNA orRNA. These enzymes are called nucleases. The RNA-degrading enzymesbelong to these nucleases, the RNases, and the DNA-degrading enzymes,the DNases. If e.g. DNA is to be cleaned, a RNase can be used during thecleaning method, which decomposes the RNA molecules into smallfractions. These methods are generally used for e.g. plasmid isolationor cleaning of genomic DNA. DNA contaminations in RNA preparations arealternatively hydrolysed with DNase I. This method is also generallyknown.

On the other hand, chemical methods can be used which utilise thedifferences in the chemical properties of RNA or DNA. A number of solidphase cleaning methods are counted amongst these. The solid phase cane.g. be an ion exchanger, as for example described in U.S. Pat. Nos.5,990,301 and 6,020,186, or it can be a porous matrix, as is describedin e.g. U.S. Pat. Nos. 6,180,778 and 5,496,562.

Other cleaning methods concern the different solubility behaviours ofRNA or DNA. The cleaning of RNA in the presence of aqueous solution of achaotropic salt and acidic phenol is counted amongst these, wherebygenomic DNA enriches in the inter phase and RNA remains in aqueoussolution (Chomczynski P. & Sacchi N., 1987, Anal Biochem. 1987 April;162(1):156-9, “Single-step method of RNA isolation by acid guanidiniumthiocyanate-phenol-chloroform extraction”).

Other methods are based on the selective precipitation of RNA or DNA.Examples for this have already been described above in connection withthe decomplexing of inhibiting biomolecules or the stabilisation ofbiomolecules.

These methods also include a separate method step, with which therelative composition of the different biomolecules, in particulardifferent nucleic acids or proteins is changed considerably to achievethe desired effect. The practicability of the method can depend if thereagant used for the separation has a negative effect on the desireddetection reaction, whereby the number of reagents available for acertain sample preparation as e.g. for an analysis method is restricted.Every method step for the separation of a sample also has acontamination risk in addition to the additional costs, which makes anextremely clean and controlled operation necessary.

With regard to different aspects, there is thus a need for a furtherimprovement of the sample preparation of samples containing biomoleculesand improved processing, preparation, and analysis methods ofbiomolecules.

SUMMARY OF INVENTION

The present invention solves this object with the method for the samplepreparation for a successive preparation, processing or analysis methodaccording to claim 1, the method for the lysis of a biological sampleaccording to the independent claim 2, the analysis method according toclaim 16, the method for stabilisation of nucleic acids and/or proteinsaccording to claim 20, the analysis method according to the independentclaim 35, the method for the reduction of inhibiting effects in a sampleaccording to the independent claim 41, the analysis method according tothe independent claim 57, the method for the selective masking accordingto the independent claim 64, and the differential analysis methodaccording to claim 76.

Further advantageous aspects, details and characteristics of the presentinvention result from the dependent claims, the description, theexamples, and the figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: a diagram in which the Delta CT values of different sampleswhich were lysated with and without a nitrogenous compound (additives)are compared.

FIG. 2: a diagram for the clarification of the increase of the RNA yieldwhich is facilitated with one embodiment of the lysis method accordingto the invention.

FIG. 3: also a diagram for the clarification of the increase of the RNAyield which is facilitated with one embodiment of the lysis methodaccording to the invention.

FIG. 4: a diagram showing the stabilising effect of different additivesof one embodiment of the stabilisation method according to theinvention.

FIG. 5: a diagram showing the stabilising effect of different additivesduring the use of different concentrations in different cell cultures inone embodiment of the stabilisation method according to the invention.

FIG. 6: the result of a gel analysis of different cell lysates.

FIG. 7: a diagram in which is shown the dependence of the Delta Ctvalues on the incubation time.

FIG. 8: a diagram in which is shown the dependence of the Delta Ctvalues on the cell number.

FIG. 9: a diagram showing the improved accessibility of gDNA by use ofdifferent additives in lysates which are obtained according to anembodiment of the method according to the invention for the reduction ofinhibiting effects.

FIG. 10: a diagram showing the improved accessibility of gDNA for DNaseI by use of different additives in lysates which are obtained accordingto an embodiment of the method according to the invention for thereduction of inhibiting effects.

FIG. 10.a.1: and

FIG. 10.a.2: the connection between the Ct value and the factor by meansof idealised hypothetic values.

FIG. 11: a diagram showing the concentration dependence of the measuredDelta Ct value.

FIG. 12: a diagram showing the measured Delta Ct values during the useof cleaned DNA in an embodiment of the method according to the inventionfor the reduction of inhibiting effects.

FIG. 13: a diagram showing the improved accessibility of gDNA and RNA inlysates in the presence of distamycine D according to the invention.

FIG. 14: a diagram showing the improved accessibility of RNA incomparison to DNA in cell lysates with different additives according tothe invention.

FIG. 15: a diagram showing the effect of the differential masking ofgDNA compared to RNA in cell lysates according to the invention withdifferent concentrations of spermine by means of the measured Delta Ctvalues.

FIG. 16: a diagram showing the effect of the differential masking ingDNA in cell lysates according to the invention with the use ofdifferent additives.

FIG. 17: a diagram showing the effect of the differential masking ofgDNA according to the invention, normalised to RNeasy preparations.

FIG. 18: a diagram showing the concentration dependence of the effect ofthe masking of gDNA in cell lysates according to the invention.

FIG. 19: a diagram showing the effect of the masking of RNA according tothe invention.

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT

Before the individual aspects of the present invention are described,the following terms are explained in the following, as they areunderstood in the present invention.

Organisms: Organisms are defined as any form of casings containingnucleic acids and/or proteins. These include e.g. viruses, phages,cells, cell formations or entire organisms. These organisms can be usedlive, dead or in their resting state. These organisms can be insolution, pelleted, or can also be associated with solid phases orbound. When “organisms” is mentioned within the scope of the presentinvention, it could be several organisms of the same type, severalorganisms of a different type, or also a single organism. The organismscan be founded on archaebacteria, procaryonts or eucaryonts. They canhave animal, vegetable or endosymbiontic (e.g. also mitochondria orplasides) origin. Amongst the organisms in the sense of the presentinvention are e.g. individual cells, cell assemblies, tissue or wholeanimals or whole plants, cultivated cells, excretion products orsecretions, e.g. stabilised and non-stabilised blood, serum, plasma,tissue fluids, sperm, swabs, sputum, saliva, tear fluid, urine,excrements, hair or hair roots, hair dandruff, buccal swabs, buffy coat,etc.

Cellular substance: Cellular substance within the scope of the presentinvention is a heterogenous material mixture which occurs withinorganisms or which can be delivered into the environment, as e.g. tissuefluids, plasma, saliva, sputum, secretions etc. The cellular substancecontains cell contents as e.g. nucleic acids, proteins and otherpolymers and metabolites. The substances to be assigned to the casing ofthe organism also belong to these, as e.g. casings, in particularmembranes, capsides, cell walls, extra-cellular matrices etc.

Biomolecules: Biomolecules are molecules which originate from organismsor their conversion products obtained in line with a detection method ase.g. by an amplification. Biomolecules are e.g. nucleic acid or proteinsor other molecules from organisms. The biomolecules can be obtained bye.g. the lysis of organisms.

Nucleic acid: Nucleic acid (NA) is conceived to be deoxyribonucleic acid(DNA), ribonucleic acid (RNA) or peptide nucleic acid (PNA) within thescope of the present invention. Deoxyribonucleic acid (DNA) andribonucleic acid (RNA) occur naturally in organisms, but they can alsooccur outside of organisms or could have been added to these. The lengthof the nucleic acid can be different. The nucleic acid can be modifiedby changes. E.g., one or more of the nucleobases of the nucleic acid canbe modified. Even the sugar units in the nucleic acid can be modified(e.g. by methoxy groups) or even replaced, as for example in PNA. Thenucleic acid can contain base analogons as e.g. non-purine ornon-pyrimidine analogons or nucleotide analogons as e.g. PNA. The DNAand/or RNA can contain addenda as e.g. proteins or amino acids.

The term DNA, as understood in the present inventions, can be furthersudivided into types occurring naturally and types not occurringnaturally, whereby types not occurring naturally can also enterorganisms (for example by transfection or transformation). Genomic DNA(gDNA) contains the sequence information which contains the design ofthe organism. Partial regions, also very small partial regions from thissequence are called genomic DNA, which do not correspond to the entiresequence in line with the present invention. Genomic DNA are also theirmodified forms as understood in line with the present invention. Theterm “DNA” also includes plasmid DNA. Plasmid DNA is anextra-chromosomal DNA with an own “origin of replication”. Plasmid DNAare also their modified forms as understood in line with the presentinvention. The term “DNA”, as understood here, also includes mtDNA orptDNA. mtDNA or ptDNA is the genomic DNA from mitochondria or plastides.mtDNA or ptDNA are also their modified forms as understood here.

The term “RNA”, as understood here, includes the naturally occurring andnot naturally occurring types, whereby not naturally occurring types canenter organisms (e.g. by transfection). mRNA, hnRNA and rRNA are largeRNA molecules (50 nt to many kb), which can be produced as a copy from acoded region. mRNA or rRNA are also their modified forms as understoodin line with the present invention.

tRNA, miRNA, siRNA etc. are small RNA molecules, which are effectiveduring the translation. Every amino acid (AS) which is connected tofurther amino acids via a peptide connection in a linear or also abranched arrangement is called protein. The protein can occur asmonomer, dimer, or multimer, whereby homomers or heteromers can beformed. Proteins can be naturally occurring proteins or can be syntheticproteins. The proteins can be present in a modified form. These proteinscan be e.g. enzymes, structural proteins, receptors, ion channels andother transporters, extracellular matrix proteins, transcriptionregulators, proteins binding nucleic acid, casing and protectionproteins, storage proteins etc.

Lysis: The term “lysis” is a process in line with the present inventionwhich results in that nucleic acids and/or proteins are passed fromorganisms into the environment. The structure of the organisms canthereby be destroyed, e.g. the casing of the organism can be dissolved.With the term “lysis” is also understood, in line with the presentinvention, that cellular substances can exit from the organisms throughsmall openings, e.g. pores etc. in the casing of the organism withoutdestructing the structure of the organisms. Pores can for example beproduced by lysis reagents. Furthermore, the term “lysis” in line withthe present invention means that nucleic acids and/or proteins oforganisms, which already appear to be structurally destroyed or whichhave small openings, can be flushed out by the use of an additive. Alysate is produced by the lysis. The process of the lysis can take placeby means of enzymatic, chemical or physical lysis methods.

Enzymatic, chemical or physical lysis methods: The term “enzymatic lysismethod” in line with the invention is a process which supports the lysisof organisms or the release of biomolecules by means of enzymes. Thatis, the enzymes for enzymatic lysis methods are characterised in that itsupports a lysis of organisms or a release of biomolecules. Such enzymesare e.g. proteases, lysozymes, glucanases, peptidases, lipases,hyaluronidases, collagenases, nucleases, amylases, hydrolases,pectinases, etc. The specialised expert knows of more enzymes, whichsupport a lysis of organisms or a release of biomolecules in the senseof the present invention. These enzymes can be obtained in a classicmanner from organisms or by biotechnological methods. These enzymes arealso genetically or chemically changed enzymes, and heat-unstable orheat-stable enzymes.

The term “chemical lysis method” in line with the invention is a processwhich supports the lysis of organisms or the release of biomolecules bymeans of chemicals. These are e.g. detergents, acid, base, organicsolvents, chaotropic substances etc.

The term “physical lysis method” in line with the invention is a processwhich supports the lysis of organisms or the release of biomolecules bymeans of physical methods. These are mechanical, thermal, but also thosemethods which are based on the effect of waves and pressure differences.Mechanical lysis methods are e.g. methods which cause a shearing or acomminution as e.g. mills, knives, small canulas, sieves, mortars, orimpingement with particles or methods which can lead to a homogenisationof the sample. With the thermal lysis method, a temperature change leadsto the degradation of organisms or the release of biomolecules. Thesecan e.g. be based on heating or cooling, e.g. under the freezing point.Methods based on the effect of waves are e.g. treatments with sound orelectromagnetic waves. Pressure changes can also support the lysis, ase.g. in the form of squeezing or sudden pressure changes (e.g. Frenchpress).

The specialised expert is aware of further enzymatic, chemical orphysical lysis methods and it is also known that these methods can beused in different combinations.

Lysis buffer: The term “lysis buffer” is generally a fluid used for thelysis in line with the present invention. This fluid can be a solutionof different lysis reagents. The lysis buffer can, but does not have tocomprise a buffer system for adjusting the pH. The fluid compositionsused in the method according to the invention represent e.g. “lysisbuffers”.

Reaction system: A reaction system in line with the present invention isto be understood every form of the system, with which a component whichis contained in a sample can be modified, identified or changed in abiological, chemical or physical reaction. The reaction system containsat least a detectable amount of the component to be analysed, e.g. DNAand/or RNA.

Differential analysis: The differential analysis is a reaction system,in which a sample is used, in which at least two different components.e.g. the nucleic acids DNA and RNA are contained, and in which at leastone of the components, e.g. one of the above-mentioned nucleic acids isnot to be analysed.

Nucleic acid preparations or protein preparations: nucleic acidpreparations are nucleic acids which were obtained by the preparation ofa sample containing nucleic acid or a mixture of materials containingnucleic acid, whereby the preparation represents a method with which therelative concentration of different nucleic acid or protein speciescontained in the sample or in the mixture of materials is influenced, sothat one or more determined species of nucleic acid were enriched in thenucleic acid preparation. Amongst the preparation methods thereby aree.g. purification methods as e.g. the cleaning of nucleic acids from asample via a silica membrane (e.g. Rneasy or QIAamp®, obtained from thecompany QIAGEN GmbH, Hilden, Germany), whereby the concentration ofproteins with regard to the nucleic acid compared to the sample of themixture of materials considerably declines before the preparationmethod. An analogon applies to the protein preparation.

In the following, different nucleic acid hybridisation or sequencing andsynthesis methods are described, as they can be used in line with theanalysis method according to the invention. These methods are standardmethods, as for example described in the applications WO 01/498802 or US2002/0115851.

Binding reactions: A binding reaction is a reaction in which at leasttwo binding partners (e.g. two nucleic acid molecules in a hybridisationor two proteins in an antibody antigen interaction or protein andnucleic acid in a binding reaction) interact with one another. Bindingreactions are carried out to execute the detection reactions orquantification or to prepare this.

A sample is contacted with a probe, so that the sample can be bound bythe probe. The probe can be modified in such a manner that a simpledetection of the probe is possible. These modifications can e.g. becouplings of fluorophores, radioactive substances or enzymes.

The nucleic acid first strand is the nucleic acid strand which is formedduring the primer-dependent nucleic acid synthesis by an enzyme, as e.g.DNA or RNA polymerase, ligase etc., and which is complementary to atarget nucleic acid. The nucleic acid secondary strand is the nucleicacid strand which is formed during the primer-dependent nucleic acidsynthesis by an enzyme and is complementary to the sequence of the firststrand.

A nucleic acid which reacts in a reaction system, e.g. specificallybinds a defined primer or oligonucleotide, that is, can hybridise withthis, is seen as a target nucleic acid. The target nucleic acid servesin this example as matrice of the nucleic acid strand to be synthesisedafter the primer binding with the primer-dependent nucleic synthesis byan enzyme, e.g. DNA- or RNA-dependent DNA polymerises, whereby thesequence of the nucleic acid strand to be synthesised is complementaryto the sequence of the target nucleic acid. Specific binding doesthereby not mean that 100% of complementing has to be present betweenthe target nucleic acid and the hybridising part of the primer oroligonucleotide. Up to a maximum of 50% of the bases in the hybridisingregion between primer and target nucleic acid are not allowed to becomplementary, so as to achieve useful results. Good up to very goodresults can be achieved when no more than 30% of the bases of thehybridising part of the primer and the target nucleic acid are notcomplementary. The higher the degree of complementing between thehybridising part of the primer and the target nucleic acid, the morespecific and effective is the primer.

On one hand, the target sequence is the sequence containing the primerbinding location, and on the other hand the sequence which is in the 3′direction (downstream) of the primer binding location. A nucleic acidsequence is formed at the primer-dependent nucleic acid synthesis, whichis complementary to the target sequence.

Primers are starters for the nucleic acid synthesis. These are mostlyshort-chained, single strand oligoribo- or oligodeoxyribonucleotideswhich are complementary to a region of one single strand nucleic acidmolecule (see above) and can react with this to a double strand. Thefree 3′ hydroxy end in this double strand serves as a substrate fornucleic acid polymerases, as for example DNA polymerases, and asstarting point for the polymerisation of the entire single strand to adouble strand. Primers are generally defined as an oligomeric startermolecule, which can bind sequentially to the target nucleic acid. Thesequence of the target nucleic acid which binds the primer, is calledprimer binding location. A primer can thereby also bind different targetnucleic acids, when these all contain the same or a similar sequence asprimer binding location. A first or primary primer P1 is defined as“anti-sense primer” and a second or secondary primer P2 as “senseprimer”.

A “sense primer” which is either a secondary primer P2 added to thereaction from outside or a primer formed by the backfolding of thenucleic acid first strand (so-called “hairpin loop”) is understood to bea secondary strand synthesis primer.

A primer binding location is the sequence of the target nucleic acidwhich can bind the primer by hybridisation. The sequence of the primerbinding location is at least up to 30%, preferably at least 50%,particularly preferably 100% complementary to the sequence of theprimer.

The hybridising part of the primer is the sequence part of the primerwhich hybridises to the primary target molecule and which iscomplementary to the sequence of the primer binding location of theprimer target molecule in at least 50% of the bases. The primary targetmolecule is the nucleic acid molecule that is introduced into theenzymatic reaction. It is not a product of this reaction.

The primer-dependent nucleic acid synthesis catalysed by enzymes, asparticularly DNA and RNA dependent DNA polymerases is a key reactionwith the cDNA synthesis, DNA sequencing and with application methods ase.g. the polymerase chain reaction (PCR)/RT-PCR or the isothermalamplification methods NASBA (nucleic acid sequence based amplification),3SR (self-sustained sequence replication; contains the use of RNase H),2SR (self-sustained sequence replication; similar to 3SR, but withoutthe use of RNase H), TMA (transcription mediated amplification), SDA(strand displacement amplification), LCR (ligase chain reaction) andrelated methods. The efficiency of the primer-dependent nucleic acidsynthesis is influenced by the activity of the enzyme for the nucleicacid polymerisation (e.g a DNA polymerase), by the target nucleic acidand by the efficiency and specificity of the primer hybridisation. Inthe following, some application examples for primer-dependent nucleicacid synthesis processes are described in more detail.

Primer-dependent nucleic acid synthesis reactions can be found e.g. inthe first and secondary strand cDNA syntheses, the DNA sequencing,mutagene processes based on primer binding and other methods.Sequence-specifically started nucleic acid synthesis reactions arethereby carried out using enzymes, as e.g. RNA- or DNA-dependentpolymerases, whereby the sequence-specifically started DNA synthesisreactions contain the following steps:

1. Sequence-specific hybridisation of a first primer P1 to one sequenceof the target nucleic acid (RNA or DNA) complementary to this: and 2.extension of the primer P1 by the catalytic insert ofdeoxyribonucleotides to the free 3′-OH end of the primer P1 to beextended by means of an enzyme as e.g. a RNA-dependent or DNA-dependentDNA polymerase, whereby the target nucleic acid serves as a matrice, andthe primer P1 altogether, or at least in the 3′-region, contains asequence which is complementary to a certain sequence of the targetnucleic acid and can hybridise at this target-sequence in asequence-specific manner, and whereby the primer P1 can contain asequence in the 5′-region which is not complementary to the targetnucleic acid and which cannot hybridise at the target nucleic acid andcan contain additional functions. The synthesis runs to the end of thetarget nucleic acid (matrice) or can be interrupted before the end,whereby the first strand nucleic acid synthesis is ended.

3. The nucleic acid secondary strand synthesis starts through thesequence-specific hybridisation of a secondary strand synthesis primer(ZP). The secondary strand synthesis primer can be a separate primer P2introduced into the reaction, a degradation product of the targetnucleic acid, or a primer (hairpin loop) formed by the backfolding ofthe nucleic acid first strand.

4. Extension of the ZP by the catalysed integration of nucleotides tothe free 3′-OH end of the ZP to be extended by means of an enzyme,whereby the nucleic acid first strand of the target nucleic acid servesas matrice; the ZP contains, altogether, or at least in the 3′-region, asequence which is complementary to a certain sequence of the targetnucleic acid and which can hybridise at this in a sequence-specificmanner, and the ZP can contain a sequence in the 5′-region which is notcomplementary to the target nucleic acid, and cannot hybridise at thetarget nucleic acid as a consequence thereof or can comprise a sequencedifferent to the primer P1.

The primer-dependent synthesis reaction is a key reaction, even with thesequencing. The method of the nucleic acid sequencing essentiallyfollows the method described previously under primer-dependent nucleicacid synthesis reaction and is limited to the steps (1) and (2),whereby, in the case of a DNA synthesis, a mixture ofdeoxyribonucleotides and dideoxyribonucleotides is used for thecatalytic integration by enzymes, as e.g. RNA- or DNA-dependentpolymerases.

The sequence-specifically started nucleic acid synthesis reactions arethereby carried out for the sequencing by enzymes, as for example RNA-or DNA-dependent DNA-polymerases, whereby the sequence-specificallystarted DNA sequence reactions contain the following steps:

-   -   sequence-specific hybridisation of a primer P1 to a sequence of        the target nucleic acid (RNA or DNA) complementary to this.

2. extension of the primer P1 by the catalysed integration ofdeoxyribonucleotides and dideoxyribonucleotides to the free 3′-OH end ofthe primer P1 to be extended by an enzyme, e.g. a RNA-dependent orDNA-dependent DNA polymerase, whereby the target nucleic acid serves asa matrice, and the primer P1 contains, altogether, or at least in the3′-region, a sequence which is complementary to a certain sequence ofthe target nucleic acid and can hybridise to this target sequence in asequence-specific manner, and whereby the primer P1 can contain asequence in the 5′-region which is not complementary to the targetnucleic acid and which cannot hybridise at the target nucleic acid andcan contain additional functions.

Primer-dependent nucleic acid synthesis reactions are also found atfirst and secondary strand DNA syntheses of the polymerase chainreaction (PCR). The sequence-specifically started DNA synthesisreactions are thereby carried out by heat-stable RNA- and/orDNA-dependent DNA-polymerases, whereby the sequence-specifically startedDNA sequence reactions contain the following steps:

-   -   initial thermal denaturing of the target nucleic acid;    -   sequence-specific hybridisation of two primers P1 and P2 to a        sequence of the target nucleic acid complementary to this;    -   extension of the primers P1 and P2 by the catalysed integration        of deoxyribonucleotides to the free 3′-OH end of the primers P1        and P2 to be extended by a heat-stable RNA-dependent or        DNA-dependent DNA polymerase, whereby the target nucleic acid        serves as matrice;    -   the primer extension products on their part serve in as matrice        for the primer hybridisation of the primers P1 and P2 after        entry into step (1); and 5. the steps (1) to (4) can be repeated        arbitrarily, and the nucleic acid with the desired properties        can thus be synthesised, whereby the primers P1 and P2 contain,        altogether, or at least in the 3′-region, a sequence which is        complementary to a certain sequence of the target nucleic acid        and can hybridise to this target sequence in a sequence-specific        manner, and whereby the primers P1 and P2 can contain a sequence        in the 5′-region which is not complementary to the target        nucleic acid and which cannot hybridise at the target nucleic        acid and can contain additional functions.

Sequence-specifically started nucleic acid synthesis reactions arefurther components of isothermal, exponential nucleic acid amplificationmethods based on in-vitro transcription as e.g. NASBA (nucleic acidsequence based amplification), 3SR (self-sustained sequencereplication), 2SR (self-sustained sequence replication similar to 3SR,but without use of RNase H), TMA (transcription-mediated amplification),and similar methods. With these methods, primers are used. RNA- andDNA-dependent DNA polymerases and suitable reaction conditions, wherebythe exponential nucleic acid amplification methods comprise thefollowing steps:

-   -   production of a single reaction medium, which contains a target        nucleic acid, a first primer P1, a second ZP, an RNA-dependent        DNA polymerase, a DNA-dependent DNA polymerase, a DNA-dependent        RNA polymerase, ribonucleotides and deoxyribonucleotides;    -   setting reaction conditions, so that amplification cycles can be        maintained, whereby    -   the first strand synthesis is carried out complementary to the        target nucleic acid by the hybridisation of a primer P1 to a        complementary target sequence, followed by an extension of the        primer P1 by deoxyribonucleotides using a RNA- or DNA-dependent        DNA polymerase, whereby the target nucleic acid can be either a        DNA or a RNA, and    -   the synthesis of the secondary strand DNA is carried out        complementary to the first strand DNA by the enzymatic, thermal        or chemical denaturing or degradation of the target nucleic acid        of the first strand DNA and the hybridisation of a ZP to the        complementary first strand DNA, followed by an extension of the        ZP by deoxyribonucleotides using a RNA- or DNA-dependent DNA        polymerase, whereby the primers P1 and ZP contain, in the        3′-region, a sequence which is complementary to a certain        sequence of the target nucleic acid and can hybridise at this        target sequence in a sequence-specific manner, and whereby at        least one of the primers P1 or ZP or both primers contain a        sequence in the 5′-region which is not complementary to the        target nucleic acid and which cannot hybridise at the target        nucleic acid and contains a DNA-dependent RNA polymerase        promoter sequence, from which can be carried out an in-vitro        transcription of the DNA molecule synthesised in steps (1)        to (4) using DNA-dependent RNA polymerase and ribonucleotides,        whereby the generated in-vitro transcripts again serve as        matrice and again enter DNA first and secondary synthesis under        sequence-specific hybridisation of primer P1 and ZP, followed by        in-vitro transcription. An exponential amplification of the        nucleic acid is achieved in this manner.    -   Sequence-specifically started nucleic acid synthesis reactions        are further components of linear, isothermal nucleic acid        amplification methods based on in-vitro transcription. These        methods are carried out using sequence-specifically binding        primers. RNA- and DNA-dependent DNA polymerases and RNA        polymerases with suitable reaction conditions, whereby the        isothermal, linear nucleic acid amplification methods comprise        the following steps:

production of a single reaction medium, which contains a target nucleicacid, a first primer P1, a second ZP, a RNA-dependent DNA polymerase, aDNA-dependent DNA polymerase, a DNA-dependent RNA polymerase,ribonucleotides and deoxyribonucleotides.

carrying out the first strand synthesis complementary to the targetnucleic acid by the hybridisation of a primer P1 to a complementarytarget sequence, followed by an extension of the primer P1 bydeoxyribonucleotides using a RNA- or DNA-dependent DNA polymerase,whereby the target nucleic acid can be either a DNA or a RNA;

carrying out the synthesis of the secondary strand DNA complementary tothe first strand DNA, by the enzymatic, thermal or chemical removal ofthe target nucleic acid from the first strand DNA and the hybridisationof a ZP to the complementary DNA of the first strand. The nucleic acidsecondary synthesis begins by the sequence-specific hybridisation of asecond ZP, a degradation product of the target nucleic acid or by thebackfolding of the nucleic acid first strand to the sequence of thenucleic acid first strand of the target nucleic acid complementary tothis. An extension of the ZP by deoxyribonucleotides follows with theuse of a RNA- or DNA-dependent DNA-polymerase, whereby the primers P1and ZP contain, in the 3′-region, a sequence which is complementary to acertain sequence of the target nucleic acid and can hybridise to thistarget sequence in a sequence-specific manner, and whereby at least oneof the primers P1 or ZP or both primers contain a sequence in the5′-region which is not complementary to the target nucleic acid andwhich cannot hybridise to the target nucleic acid and contains aDNA-dependent RNA polymerase promoter sequence, from which can becarried out an in-vitro transcription of the DNA molecule synthesised insteps (1) to (3) by the use of DNA-dependent RNA polymerase andribonucleotides. A linear amplification of the nucleic acid is achievedin this manner.

Strand Displacement Amplification (SDA): SDA is a generic term for anumber of methods which lead to the amplification of nucleic acid. Thereactions contain at least the nucleic acid to be amplified, a suitablebuffer, primer, dNTPs and a polymerase. The reaction leads to a nucleicacid synthesis, whereby a double-strand is freed to be able to use asingle strand generated in that manner as matrice. The freeing can becarried out by the polymerase itself (original SDA). The freeing of thedouble strand can alternatively be carried out by means of a helicase(helicase-dependent amplification) If primers are used which comprisechance sequence, the reaction is called multiple displacementamplification (MDA). A method was developed by VanNess, in which theprimers originate from first strand breaks of the target nucleic acid tobe amplified (US patent application 2003/138800, “Exponentialamplification of nucleic acids using nicking agents”). A method wasdeveloped by the company NUGen (USA), where RND/DNA fusion primers areused. Another SDA reaction uses circular DNA for the amplification(rolling circle amplification). DNA is synthesised hereby. A similarmethod amplifies RNA (rolling transcription amplification).

Primer-independent synthesis reactions: Primer-independent synthesisreactions are reactions which do not need a primer. An example of aprimer-independent synthesis reaction is the transcription reaction.With a transcription reaction is synthesised a transcript, starting froma gene which contains a suitable promoter for a RNA polymerase, in thepresence of nucleotides, a suitable reaction environment and RNApolymerase. This takes place without the use of a primer. A number oftranscripts are read from a gene and synthesised.

A further example for a primer-independent synthesis reaction is thetranslation reaction. Here, a RNA transcript is brought into contactwith a translation apparatus. This consists of ribosomes and all furthercomponents which are necessary to produce proteins or polypeptides.Amongst these are e.g. tRNAs, aminoacyl-tRNA-synthetases etc. If atranscript is brought into contact with this reaction solution, proteinscan be produced by means of this primer-independent reaction.

In the following, further reaction systems are described, as they can beused in line with the analysis method according to the invention.

Enzymatic tests are reaction systems, in which catalytically effectivebiomolecules can be measured with the help of their catalytic activity.Amongst these are e.g. tests of enzymes such as dehydrogenases,hydrolases, polymerases, phosphorylases, phosphatases, kinases, etc.

Use of surfaces of biomolecules: This is understood to be aquantification, detection, enrichment or depletion of biomolecules usingthe specific characteristics of their surface. Amongst these are e.g.detections of biomolecules with the help of antibodies, aptameres orbinding partners, cofactors, proteins of multienzyme complexes or alsoprotein or nucleic acid for detections of nucleic acid proteininteractions.

Degradation of biomolecules. This is understood to be the destruction ofat least one property of a biomolecule. Enzymes can e.g. only reduce thesize of biomolecules when the enzymes recognise the structure of thetarget molecule. The nitrogenous compounds according to the inventioncan also contribute to this.

In general, the present invention relates to a method for the samplepreparation for a successive preparation, processing or analysis methodof a sample containing at least one species of nucleic acid and/or aspecies of protein, whereby the method comprises the following steps:

-   -   providing a sample which comprises at leas one species of a        nucleic acid and/or of a protein,    -   contacting the sample with a fluid or solid composition to        generate a fluid sample preparation, whereby the composition        contains at least a nitrogenous compound, which is chosen from        the group consisting of a) polyamines, b) amino acids, and        oligo- and polypeptides, c) nitrogenous heterocyclic compounds        including homo or hetero polymers, which comprise these        nitrogenous compounds, d) amines of the type R¹R²NR³, whereby        R¹, R² and R³ are chosen independently from one another from the        group consisting of H, C₁-C₅-alkyl groups and aryl groups,        whereby R¹, R² and R³ are not H simultaneously, e) carboxylic        acid amides, f) inorganic ammonium salts, g) ammonium groups        containing inner salt compounds, h) antibiotica binding nucleic        acid, i) compounds, which bind in the small cavity of the        DNA, j) nitrogenous compounds chosen from the groups described        under a-I with an additional derivation, and mixtures of two or        more of these compounds.

The sample can thereby be an organism or a mixture of materialscontaining nucleic acid and/or protein. The fluid sample preparationproduced in step B) comprises a pH between 7.1 and 14, preferably a pHbetween 7.1 and 12, and particularly preferred a pH between 7.4 and 10in all embodiments of the method according to the invention.

As a processing method is to be understood every enzymatic, chemical orphysical conversion of the biomolecules present in the sample. Specialaspects of this method will be explained in the following with referenceto special embodiments as further aspects of this invention. Thesespecial embodiments relate to, as explained in the following, a methodfor the lysis of a biological sample, a method for the stabilisation ofnucleic acids and/or proteins, a method for the reduction of inhibitingeffects in a sample containing nucleic acids and/or proteins, a methodfor the selective masking of nucleic acids in a sample and analysismethods which respectively build on these methods.

Accordingly, one aspect of the present invention relates to a method forthe lysis of a biological sample which contains at least one species ofa nucleic acid and/or at least one species of a protein in a casing. Inparticular, biological casings as e.g. membranes, capsides or cell wallscan be used as casings, but the casings are not limited to these. Thesample is brought into contact with a fluid or solid composition for theproduction of a lysate, which contains at least one nitrogenouscompound, which is selected from the group consisting of:

-   -   polyamines, b) amino acids and oligo and polypeptides, c)        nitrogenous heterocyclic compounds, including homo or        heteropolymeres, which comprise these nitrogenous compounds, d)        amines of the type R¹R²NR³, whereby R¹, R² and R³ are chosen        different from one another from the group consisting of H,        C₁-C₅-alkyl groups and aryl groups, whereby R¹, R² and R³ are        not H simultaneously, e) carboxylic acid amides, f) inorganic        ammonium salts, g) ammonium groups containing inner salt        compounds, h) antibiotica binding nucleic acid, i) compounds        which bind in the small cavity of the DNA, j) nitrogenous        compounds chosen from the groups described under a-i with an        additional derivation and mixtures of two or more of these        compounds. Amongst “sample which contains at least one species        of a nucleic acid and/or at least one species of a protein in a        casing” are organisms as understood in line with the present        invention. Whether the sample is contacted with a fluid or solid        composition, depends if the sample contains sufficient fluid, so        that a sufficiently fluid lysate is obtained by the lysis for        the further use. The composition will preferably be fluid. The        nitrogenous compound can thereby be dissolved in a solvent or be        present in a suspended manner.

It is possible with the lysis method according to the invention, totransfer higher amounts of nucleic acids and/or proteins into the lysatecompared to standard lysis methods. It is assumed that the nitrogenouscompound leads to a more effective dissolving of the casings of theorganisms contained in the sample, whereby higher amounts of the cellcontents can reach enter the lysate.

In a preferred embodiment of this method, the lysis is carried out insuch a manner that the at least one species of the nucleic acid and/orprotein is dissolved or suspended in the produced lysate. So as toachieve that at least one species of the nucleic acid and/or protein isdissolved or suspended in the produced lysate, the lysis conditions haveto be chosen in such a manner that a precipitation of the at least onenucleic acid and/or of the protein does not occur. The terms “dissolved”and “suspended” in line with the present invention mean that the atleast one species of nucleic acid or protein remain in the fluid phaseof the sample preparation, for example the lysate, and are therebyaccessible for a successive analysis by a corresponding detection oranalysis method. This is in contrast to precipitated components of thelysate, which cannot be transferred directly to a detection or analysismethod, but which first have to be transferred into the fluid phase bycorresponding method steps. The type of sample with which the lysis iscarried out has to be considered hereby. Possible further components inthe composition which contains the nitrogenous compound also have to beconsidered here, and possibly the suitable conditions for a certainsystem of sample and composition have to be determined by means ofsimple routine examinations. This can for example take place in that itis observed if a precipitation takes place with the lysis. If this isthe case, the precipitate can be checked for its composition usinganalysis methods and procedures used by default, in particular if theprecipitate contains the species of nucleic acid and/or protein to bedissolved/suspended. In particular, in this embodiment, theconcentration of the nitrogenous compound in the composition has to bechosen in such a manner that the nucleic acid remains dissolved orsuspended in the lysate and the nitrogenous compound thereby does noteffect a precipitation of the species of nucleic acid and/or protein inthe lysate.

It is for example possible that the lysate can be subjected to asuccessive analysis of the species nucleic acid and/or the protein in areaction system in that at least one species of nucleic acid and/orprotein remains dissolved and/or suspended in the lysate. Other cellcontents, which are not to be analysed, can be precipitated during thelysis and thus be removed from the fluid sample volume. The at least onespecies of nucleic acid and/or protein is thereby a species which isprovided for a successive preparation, processing or analysis method.

In a further embodiment, the lysis is carried out in the presence of acarrier material for the immobilisation of the at least one species ofnucleic acid. Thereby, usual carrier materials can be used, which areusually used in the nucleic acid or protein analysis, e.g. microarraysor so-called “beads”. “Beads” are microparticles which have a surface towhich molecules can bind. Such a surface can e.g. be achieved by acorresponding surface treatment. Examples of such materials areOligotex® and Liquichip®, obtained from the company QIAGEN, Hilden,Germany.

In a further embodiment of the method according to the invention, thesample contains at least two species of the group consisting of nucleicacids and proteins. The lysis is carried out in such a manner that thetwo or more certain species of nucleic acid and/or proteins arecontained in the produced lysate, in particular, that these aredissolved or suspended in the lysate. For example, nucleic acids such asDNA and RNA, in particular gDNA and RNA can be contained in the lysatein the method. Alternatively, proteins can selectively be kept insolution/suspension. As described above, the type of the sample and thedifferent lysis reagents have to be considered, in particular the amountof the used nitrogenous compound.

In a further embodiment of the invention, the sample contains at leasttwo species from the group consisting of nucleic acids and/or proteinsand the generation of the sample preparation or the lysis is carried outin such a manner that several determined species of nucleic acid and/orprotein are dissolved and/or suspended in the produced lysate. Thereby,either the species of nucleic acids contained in the sample or allspecies of proteins contained in the solution can be dissolved and/orsuspended. This means that essentially no precipitation takes placeduring the lysis, as is used e.g. for the removal of nucleic acids orproteins from lysates. If the sample contains several species of nucleicacid and/or proteins, and two, several or all of these species shallremain dissolved and/or suspended in the lysate after the lysis, it isparticularly preferred that the relative concentration of thesedifferent species of nucleic acids and/or proteins do not change withregard to one another by the lysis and thereby the relativeconcentration of these species in the lysate remains essentiallyunchanged with regard to the relative concentration of this species inthe sample. It again applies, as already disclosed above, to considerthe type of the sample and the different possibly used lysis reagantsand the type of the used nitrogenous compound during the execution ofthe lysis and that suitable routine tests have possibly to be carriedout, to determine suitable conditions for a given sample type.

By the above-described lysis methods, where at least two species ofnucleic acid and/or proteins are dissolved and/or suspended in thelysate, it is possible to use the lysate containing these species forthe analysis or the detection of every one of these species in asuccessive analysis or detection method.

The nitrogenous compound can thereby, in addition to a more effectivelysis, which leads to an increased concentration of the desired speciesof nucleic acid and/or protein in the lysate, also have a stabilisingeffect on the species of nucleic acid and/or protein dissolved and/orsuspended in the lysate. Furthermore, the inhibiting interactions andeffects in the lysate can be decreased or suppressed by the use of thenitrogenous compound in the composition used for the lysis. Furthermore,it is possible by the use of the nitrogenous compound, to mask a certainspecies of nucleic acid in the lysate, so that this species of nucleicacid does not have any disadvantageous effects on the analysis ordetection method of a further species contained in the lysate. Thesespecial additional aspects are discussed in more detail in thefollowing.

In a further preferred embodiment of the method, DNA and/or RNA aredissolved and/or suspended in the lysate as nucleic acid species. Inanother embodiment, one or more species of protein are dissolved and/orsuspended in the lysate.

In a further preferred embodiment of the lysis method according to theinvention, the composition used for the lysis comprises, in addition tothe nitrogenous compound, further lysis reagants, at least one reagantfrom the group of the complexing agents, detergents, substances for thevolume restriction and/or solvents. In particular EGTA (ethyleneglycol-bis(2-amino ethylether)-N,N,N′,N′-tetra acetic acid) and EDTA(ethylene dinitrilotetra acetic acid) are considered as complexingagents. Possible detergents are in particular triton x 100 (polyethyleneglycol-tert.-octylphenylether), Nonidet-P40 (Nonylphenyl-polyethyleneglycol), n-Ocytlglucosid and N-Cetyl-N,N,N-trimethyl-ammonium bromide.As substances for the volume restriction are in particular consideredpolyethylene glycoles of different chain lengths. H₂O or phenol ormixtures thereof are preferably used as solvents. The complexing agentsare preferably used in an amount, so that they are respectively presentin the sample preparation, e.g. the lysate in a concentration of 0.1 to10 mM. If fluid compositions are used as compositions used for thelysis, that is, a lysis buffer, the complexing agents are respectivelypreferably present in a concentration of 0.1 to 10 mM. The detergentsare preferably used in an amount, so that they are respectively presentin the sample preparation, e.g. the lysate in a concentration of 0.01-10vol %. If a lysis buffer is used, the detergents are preferably 0.01 to10 vol % of the lysis buffer. The reagants for the volume restrictionare preferably used in an amount, so that they are respectively presentin the sample preparation, e.g. the lysate in a concentration of 0.01-5vol %. If a lysis buffer is used, it preferably contains between 0.01and 5 vol % reagants for the volume restriction. The lysis reagants arepreferred as a solution, but they can also be added differently, e.g. inthe form of a solid substance. For the present invention, lysis buffersare particularly used as compositions, consisting of H₂O as solvent, atleast one of the above-mentioned nitrogenous compounds as additive andoptional complexing agents, detergents, and/or substances for the volumerestriction.

In particular, lysis buffer can be used, which comprise all of thesecomponents. A further aspect of the present invention accordinglyrelates to compositions for the lysis of a biological sample, wherebythe sample comprises at least one nitrogenous compound used in line withthe different methods according to the invention and at least a furtherlysis reagant, as described above in connection with the lysis methodaccording to the invention.

The lysis can further be carried out under mechanical effect or withenzymatic support. As a means for the mechanical support are consideredmortars, the application of high pressure, narrow capillaries and theuse of filter units. An enzymatic support of the lysis can for examplebe supported by the use of proteases, lysozymes, cellulases, pectinases,whereby the degradation of the structure of the organisms in the sampleis supported further.

The lysis can be designed more efficiently by this support, that is, theyield of nucleic acid and/or protein in the lysate can be increased oraccelerated. It is further possible that the sample is washed with awashing buffer, in particular a hypotonic washing buffer, prior to thelysis.

In a preferred embodiment of the lysis method according to theinvention, the amount of the used nitrogenous compound is chosen in sucha manner that the concentration of the nitrogenous compound in thegenerated lysate is between 0.001 mM to 1 M, preferably between 0.001 to100 mM, particularly preferably between 0.001 to 30 mM, 0.001 to 20 mM,and specially 0.001 to 19 mM or 0.001 to 15 mM. During the use ofheterocyclic compounds as the nitrogenous compound, in particular ofimidazole, the amount of the compound can be chosen so that aconcentration of 0.01 to 20 mM of imidazole is adjusted in the lysate,particularly preferred from 0.01 to 15 mM. For compounds comprisingamino functionalities, it usually applies that the concentration of thenitrogenous compound can be lower, the more amino functionalities arecontained in the nitrogenous compound, which can interact with thenucleic acid or the protein.

In a further preferred embodiment of the lysis method according to theinvention, the at least one nucleic acid species is a DNA species. In afurther preferred embodiment of the lysis method according to theinvention, the at least one nucleic acid species is a RNA species. In afurther preferred embodiment of the lysis method according to theinvention, the at least one species of biomolecule is a protein species.

In a further preferred embodiment of the lysis method according to theinvention, the nitrogenous compound is chosen from the group consistingof:

-   -   polyamines, which are preferably selected from the group        consisting of open-chained and cyclic polyamines with 2, 3, 4, 5        or 6 amino groups. The term “polyamine” is to be understood in        line with the invention in particular compounds which comprise a        saturated carbon chain with amino group ends. The amino group        ends can be primary (H₂N—), secondary (R₁NH—) oder tertiary        amino groups (R₁R₂N—) and can be part of a cyclic group. The        remainders R₁ and R₂ here can be C₁-C₅-alkyl groups independent        from one another. The amino group ends are preferably primary or        secondary amino groups. The saturated carbon chain can be        interrupted with a changing number of secondary (—NH—) or        tertiary (—NR₁—), preferably secondary amino groups. R₁ can        again be a C₁-C₅-alkyl group. The saturated carbon chain can for        example be open-chained, unbranched or cyclic. The carbon chain        or the single carbon chains connecting the different amino        groups are preferably alkylene groups —(CH₂)_(n)—, whereby n is        a whole number from 1 to 6, preferably from 2 or 3. The cyclic        carbon chains can be pure carbon rings and saturated nitrogenous        ring groups as e.g. piperidine or piperazine. The rings thereby        preferably contain 4 to 6 ring atoms. The nitrogenous ring        groups can be substituted at least one of the nitrogen atoms        contained in the ring with a saturated carbon chain with amino        group ends. This carbon chain can again be interrupted by        secondary or tertiary, preferably secondary amino groups. The        carbon chains are also preferably alkylene groups —(CH₂)_(n)—        here, whereby n can be a whole number from 2 to 6 and is        preferably 2 or 3. Even though polyamines with 2 to 6 amino        groups are preferred, the polyamines can also contain more amino        groups. In particular, the term polyamines are also meant to be        polymeric straight chained or branched polyamines as e.g.        polyethylene imines or vinyl amines.

As polyamines can in particular be used ethylene diamine, trimethylenediamine or putrescine, spermidine, cadaverine, diethylentriamine,spermine, triethylene tetramine, tetraethylene pentamine, pentaethylenehexamine, 1,4-Bis(3-aminopropyl)-piperazine, 1-(2-aminoethyl)piperazine,1-(2-aminoethyl)piperidine,1,4,10,13-Tetraoxa-7,16-diazacyclooctadecane,Poly(1-vinylpyrrolidon-co-2-dimethylaminoethylmethacrylate) andTris(2-aminoethyl)amine) and similar. The use of unbranched polyamineswith 2 to 6 amino groups is particularly preferred, in particularethylene diamine, trimethylene diamene or putrescine, spermidine,diethylene triamine, spermine, triethylene tetramine, tetraethylenepentamine, pentaethylene hexamine, whereby the use of spermidine isparticularly preferred. b) amino acids, in particular α-amino acids. Theamino acids can thereby be present in the D or L form or as racemate.Proteinogene and non-proteinogene, but in particular proteinogene aminoacids can be used. Polar and also apolar amino acids can be used. Theapolar amino acids thereby comprise the aliphatic (e.g. glycine,alanine, valine, leucine, and isoleucine) and aromatic amino acids (e.g.phenylalanine, tyrosine, tryptophane). Polar amino acids can compriseneutral, base and also acidic amino acids, or the amides of the acidicamino acids. The neutral amino acids can e.g. be selected from the iminoacids such as proline or the amino acids with hydroxy groups as e.g.serine and threonine or the sulfur-containing amino acids as e.g.cysteine and methionine. Furthermore, the amino acids can be selectedfrom the alkaline amino acids as e.g. lysine, arginine and histidine.The amino acids can also be selected from the acidic amino acids as e.g.asparagic acid, glutamic acid or their amides as e.g. asparagine orglutamine.

Amino acids such as arginine, proline, tryptophane and glutamic acid arepreferably used as a nitrogenous compound. In a further embodiment,amino acids are used as nitrogenous compounds, which do not comprise areducing thio group.

c) Heterocyclic compounds, which are selected from the group of the fiveor six member rings or the six member rings with anellated five memberring, whereby the five member ring, the six member ring and/or theanellated five member ring comprises 1 to 3 nitrogen atoms. The five orsix member rings and the anellated rings can be unsaturated, partiallyunsaturated or aromatic. The respective ring members can comprisesubstituents in the ring compounds, which are selected from the groupconsisting of H, C₁-C₆-alkyl groups, ═O, —OH, ═S, —SH, ═NH, —NH₂,alkyl-O—, alkyl-S—, alkylamino- and dialkylamino groups, whereby thesealkyl groups (that is, the alkyl groups in the alkyl-O—, alkyl-S—,alkylamino- and dialkylamino groups) are C₁-C₅-alkyl groups, preferablyC₁-C₃-alkyl groups. The ring members can furthermore be substituted withF—, Cl—, Br— or J. The heterocyclic compounds can, respectively in thefive or six member ring groups, comprise one or more O- or S-atoms asfurther hetero atom. Preferred heterocyclic compounds are aromaticnitrogenous 5 member ring compounds of the general formula I:

whereby X is selected from NH or S, R¹, R², and R³ are selectedindependently from one another from the group consisting of —H, —F, —Cl,—Br, -J, —OH, —SH, —NH₂, —C(═O)OH, —C(═O)NH₂, alkyl-O—, alkyl-S—,alkylamino- and dialkylamino groups, whereby these alkyl groups areC₁-C₅-alkyl groups, preferably C₁-C₃-alkyl groups. Particularlypreferred are the compounds imidazole, thiazole and aminothiazole, inparticular 2-amino thiazole.

Further preferred heterocyclic compounds are aromatic six member ringcompounds of the general formula II:

whereby X₁ is selected from the group consisting of N, O, S and CR⁴, X₂is selected from the group consisting of N, O, S and CR⁵, and X₃ isselected from the group consisting of N, O, S and CR⁶, whereby at leastone of the groups X₁, X₂ oder X₃ represents N, and R¹, R², R³, R⁴, R⁵and R⁶ are selected independently from one another from the groupconsisting of H, C₁-C₆-Alkylgruppen, —OH, —SH, —NH₂, —F, —Cl, —Br, —I,alkyl-O—, alkyl-S—, alkylamino- and dialkylamino groups, whereby thesealkyl groups (that is, the alkyl groups in the alkyl-O—, alkyl-S—,alkylamino- and dialkylamino groups) are C₁-C₅-alkyl groups, preferablyC₁-C₃-alkyl groups. X₁, X₂ and/or X₃ preferably represent N. It isfurther preferred that either only X₁ is N, or X₁ and X₂ or X₁ and X₃are N. R¹ to R⁵ are preferably selected from the group consisting of Hand C₁-C₃-alkyl, and is preferably H or methyl. The compounds2,3-dimethyl pyrazine, pyridine, and pyrimidine are particularlypreferred.

Compounds according to the general formula III are further preferred:

whereby X₁ is selected from the group consisting of N, O, S and CR³, X₂is selected from the group consisting of N, O, S and CR⁴, and R¹, R², R³and R⁴ are selected independently from one another from the groupconsisting of H, C₁-C₆-alkyl groups, —OH, —SH, —NH₂, —F, —Cl, —Br, —I,alkyl-O—, alkyl-S—, alkylamino- and dialkylamino-, whereby these alkylgroups (that is, the alkyl groups in the alkyl-O—, alkyl-S—, alkylamino-and dialkylamino groups) are C₁-C₅-alkylgruppen, preferably C₁-C₃-alkylgroups.

Either X₁ or X₂ preferably represent N. Further, when X₁ is CR⁴, X₂ canbe CR⁵. R¹, R², R³ and R⁴ preferably represent H.

Particularly preferred compounds are indazole and benzimidazole.

The heterocyclic compounds selected from the group of the nucleobasesare further preferred as nitrogenous compounds. These comprise inparticular the compounds adenine, cytosine, guanine, inosine,hypoxanthine, thymine, uracile and xanthine or the compounds which canbe built into nucleic acid as analogons or derivatives, whereby thestructure of these compounds can also comprise differences in the ring.The compounds adenine, cytosine, guanine and thymine are particularlypreferred here.

The compounds imidazole and 2,3-dimethylpyrazine, pyrimidine, guanineand guanosine show a particularly good effectiveness in the presentinvention.

Furthermore, nitrogenous heterocyclic compounds are homo or heteropolymers which comprise these nitrogenous compounds.

d) amines of the type R¹R²NR³, whereby the remainders R¹, R² and R³ arechosen independently from one another from the group consisting of H andC₁-C₃-alkyl groups, whereby applies that R¹, R² and R³ are not Hsimultaneously. The use of methylamine, ethylamine, n-propylamine,dimethylamine, diethylamine, di(n-propyl)amine, di(isopropyl)amine,trimethylamine, triethylamine, tri(n-propyl)amine, andtri(isopropyl)amine is particularly preferred.

e) carboxylic acid amides comprising the structure X—C(═O)NH₂. X isthereby selected from the group consisting of: —NH₂, C₁-C₅-alkyl,C₂-C₅-alkenyl, C₂-C₅-alkinyl or aryl, preferably phenyl or anamino-substituted aryl, H₂NC(═O)—Y—, whereby Y can be an alkylene groupof the type —(CH₂)_(n)— and whereby n is a whole number from the region0 to 10, preferably 0 to 5, or Y is a C₁-C₁₀-alkenylene group,preferably a C₁-C₆-alkenylene group, or an aryl group. When Y is aC₁-C₁₀-alkenylene group, this group can comprise one or more olefinbonds, whereby the olefin bonds can be present in the carbon chain in anisolated manner or in a conjugated manner. When Y is an aryl rest,phenyl or bophenyl groups are particularly considered. X—NH₂ preferablyrepresents —NH₂ or 2 amino phenyl.

inorganic ammonium salts, which are selected from the group consistingof ammonium sulfate, ammonium carbonate and ammonium hydrogen phoshate,

ammonium groups containing inner salt compounds, which are selected frombetaine, ectoine and trimethyl amine oxide:

antibiotics binding the nucleic acid, which are selected from the groupconsisting of distamycines, in particular distamycine D, mitomycines,norfloxacins, streptozocine, duocarmycines, actinomycines, andaminoglycisides;

and

compounds which bind in the small cavity of DNA, and which are selectedfrom the group consisting of thiazotropsine, tri-imidazole andchromomycines.

nitrogenous compound selected from the groups described under a-i, withan additional derivating. The derivating can for example be carried outby a combination of the nitrogenous compounds with inorganic or organicremainders such as sugars, phosphates, alcohols, sulfates, glutathione,lipides etc. The compounds guanosine, adenosine, cytosine, andthymindine or also antibiotica are particularly preferred here.

The preferred nitrogenous compounds described above can be used in allof the further aspects according to the invention still to be explainedin the following. The nitrogenous compounds, which find use in thepresent invention, can generally be present in a free form or in theform of suitable salts. Whether a compound is used as a free compound oras a salt can depend if the composition shall be present in a fluid orsolid form.

C₁-C₆-alkyl groups are particularly the following groups in line withthe present invention: methyl, ethyl, propyl, isopropyl, butyl,1-methylpropyl, 2-methylpropyl, 1,1-dimethylethyl, n-pentyl.1-methylbutyl, 2-methylbutyl, 3-methylbutyl, 1,1-dimethylpropyl,1,2-dimethylpropyl, 2,2-dimethylpropyl, 1-ethylpropyl, hexyl,1-methylpentyl, 2-methylpentyl, 3-methylpentyl, 4-methylpentyl,1,1-dimethylbutyl, 1,2-dimethylbutyl, 1,3-dimethylbutyl,2,2-dimethylbutyl, 2,3-dimethylbutyl, 3,3-dimethylbutyl, 1-ethylbutyl,2-ethylbutyl, 1,1,2-trimethylpropyl, 1,2,2-trimethylpropyl,1-ethyl-1-methylpropyl and/or 1-ethyl-2-methyl-propyl.

The C₂-C₅-alkenyl groups in line with the present invention areparticular the groups ethenyl (vinyl), 2-propenyl (allyl), 2-butenyl,3-butenyl, 1-methyl-2-propenyl. 2-methyl-2-propenyl, 2-pentyl, 3-pentyl,4-pentyl, 1-methyl-2-butenyl, 2-methyl-3-butenyl, 3-methyl-3-butenyl,1,1-dimethyl-2-propenyl, 1,2-dimethyl-2-propenyl, und1-ethyl-2-propenyl.

The C₂-C₅-alkinyl in line with the invention are in particular ethinyl.2-propinyl (propargyl), 2-butinyl, 3-butinyl, 2-pentinyl, 3-pentinyl,4-pentinyl, 3- and methyl-2-butinyl.

The choice of the nitrogenous compound which is used for the lysis, ispreferably adjusted to the solvent used in the lysis buffer. It isthereby preferred that the nitrogenous compound is soluble in thesolvent in such a measure that concentrations of the compound arepossible in the solvent in the respective desired region.

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of nucleic acid and/or atleast one species of protein in a sample, comprising the steps:

-   -   generation of a lysate according to the lysis method according        to the invention, and use of the lysate in a reaction or        reaction sequence suitable for the detection of the at least one        species of protein.

The detection accuracy of the analysis method is improved by theimproved lysis, as higher concentrations of the respective nucleic acidand/or protein are achieved in the sample compared to usual analysismethods.

The lysate is preferably used directly without carrying out furthermethod steps for the reduction of the number of species of nucleic acidand/or proteins contained in the sample preparation or that furthersteps for the removal of materials which effect the degradation ofnucleic acids and/or proteins have to be carried out from the samplepreparation or that such materials have to be inactivated. The lysate isthereby preferably used directly for the analysis or for the productionof a reaction solution suitable for the analysis, without any furtherreconditioning step.

In other cases, the lysis can be supported by the above-mentionedmethods for the physical, chemical or enzymatic lysis. Lysis methodswith physical support by heating or homogenisation of the lysate, withchemical support by use of detergents or enzymatic support by use ofproteases as e.g. protease K (if protein is not to be detected),lysozyme or also nucleases (e.g. DNase; in this case DNA cannot bedetected) as suitable.

The reaction or reaction sequence suitable for the detection of the atleast one nucleic acid can thereby be selected from the group of thenucleic acid binding reactions, in particular the nucleic acidhybridisations, in particular Northern, Southern blotting or alsohybridisation of oligo nucleotides and probes, in particular DNA probes,the group of the enzymatic modifications or polymerisations of nucleicacids, in particular sequencing reactions, in-vitro transcription,restriction endonuclease splittings, the group of the amplificationreactions, in particular PCR (polymerase chain reaction), real-time-PCRRT-PCR (reverse transcription polymerase chain reaction),real-time-RT-PCR (method based as probes and as a method that isdependent on a sequence-unspecifically binding detector molecule as e.g.SybrGreen), RT-PCR (reverse transcription polymerase chain reaction),real-time-RT-PCR (method based as probes and as a method that isdependent on a sequence-unspecifically binding detector molecule as e.g.SybrGreen), Multiplex PCR, Multiplex RT-PCR, die sondenbasierendenVerfahren der Real-Time Multiplex PCR und Real-Time Multiplex RT-PCR,NASBA (Nucleic Acid Sequence Based Amplification), 3SR (SequenceSustained Self Replication), 2SR, TMA (Transcription MediatedAmplification), MDA (Multiple Displacement Amplification) Rolling CircleAmplification, Whole-Transcriptome-Amplification,Whole-Genome-Amplification und Rolling Transcription Amplification oderLoop-mediated isothermal amplification (LAMP).

The reaction or reaction sequence suitable for the detection of the atleast one protein can be selected from the group of the protein-bindingreactions, in particular protein recognition, in particular by otherproteins, reactions based on the enzymatic activity of the protein,antibodies, aptameres, ligands, nucleic acids, in particular Westernblotting, or other substances such as gluathione and NAD, or is selectedfrom the group of the protein modification or processing, in particular(de)phosphorylation, (de)glycolysation and splitting through proteases.

All methods mentioned above can be carried out either in solution,suspension or solid phase.

In a further aspect, the present invention relates to a method for thestabilisation of nucleic acids and/or proteins, whereby this methodcomprises the following steps:

-   -   providing a sample which comprises at least one species of a        nucleic acid and/or of a protein,    -   contacting the sample with a fluid or solid composition to        produce a fluid sample preparation, whereby the composition        contains at least a nitrogenous compound, which is selected from        the group consisting of        -   polyamines, b) amino acids and oligo and und polypeptide, c)            nitrogenous heterocyclic compounds, including homo or            heteropolymeres, which comprise these nitrogenous            compounds, d) amines of the type R¹R²NR³, whereby R¹, R² and            R³ are chosen different from one another from the group            consisting of H, C₁-C₅-alkyl groups and aryl groups, whereby            R¹, R² and R³ are not H simultaneously, e) carboxylic acid            amides, f) inorganic ammonium salts, g) ammonium groups            containing inner salt compounds, h) antibiotica binding            nucleic acid, i) compounds which bind in the small cavity of            the DNA, j) nitrogenous compounds chosen from the groups            described under a-I with an additional derivation and            mixtures of two or more of these compounds.

In a further embodiment of this method, the stabilisation of nucleicacids is carried out by one or more of the claimed substances before,during or after an enzymatic, physical or chemical lysis, preferablyusing detergents and protease as e.g. proteinase K. Thus, detergentswith a concentration of 0.005 to 10% are used. Proteases as e.g. theproteinase K can be contained in the stabilised sample in aconcentration of 0.5×10⁻⁴ mAU/μl to 50×10⁻⁴ mAU/μl.

In a further embodiment of this method, the stabilisation of RNA iscarried out by one or more of the claimed substances following after anenzymatic degradation by an endonuclease as e.g. DNase. The DNase I canthus be contained in the stabilised sample in a concentration of 0.003U/μl×0.5 U/μl.

In a further embodiment of this method, the stabilisation of protein byone or more of the claimed substances is carried out following after anenzymatic degradation by nucleic acids by nucleases as e.g. RNase,DNases, benzonases etc.

In a further embodiment of this method, the stabilisation ofbiomolecules is carried out in the sample e.g. of nucleic acid orprotein by one or several of the claimed substances chosen from e.g.treatment of the at least two species of biomolecule is carried out inthe sample through a substance chosen from e.g. arginine, imidazole,proline, lysine, spermine, spermidine, glutamic acid, indazole, thymine,thymidine, guanine, guanosine, adenine, histidine, tryptophane, ammoniumsulfate or by a mixture of these.

In a further embodiment of this method, the at least one species ofnucleic acid or protein is immobilised on a carrier material before,during or after the addition of the nitrogenous compound. The materialsalready mentioned above in connection with the lysis according to theinvention can be used as carrier materials.

In an alternative embodiment of the stabilisation method according tothe invention, the sample preparation takes place in such a manner thatthe at least one species of the nucleic acid and/or of the protein isdissolved and/or suspended in the fluid sample preparation. This canparticularly be effected by the addition of suitable amounts of thenitrogenous compound to the sample. If a lysis of a biological sample iseffected by the addition of the composition, the lysis cancorrespondingly be carried out in such a manner that at least onespecies of the nucleic acid/and or of the protein is dissolved and/orsuspended in the fluid sample preparation.

A sample is, in addition to organisms, which are subjected to a lysisfor the purpose of the disintegration, every mixture of materials whichcomprises at least one species of a nucleic acid and/or of a protein.This can be a mixture of materials or only the pure nucleic acid or theprotein. These mixtures of material can be obtained e.g. through nucleicacid or protein acid preparations. Carrier materials, on which at leastone species of nucleic acid and/or protein was immobilised, can also beused as samples. The sample can thereby be present as a solid or as asolution, or it can be pure organisms or suspensions of organisms in afluid medium as e.g. cell cultures. The composition of the sample can beadded as a fluid, e.g. as a buffer solution or as a solid in dependenceof the type of the sample. Sample preparations which contain at leastone fluid phase are a fluid sample preparation. The sample preparationcan e.g. be completely dissolved or can also comprise suspendedcomponents and solid components. Cell components can for example besuspended or be present in the sample preparation in an undissolvedmanner. The sample preparation can also comprise a carrier material forthe immobilisation of nucleic acid and/or proteins.

The at least one species of nucleic acid or protein can be stabilised byaddition of the nitrogenous compound or protein in the samplepreparation, so that a direct separation of this species of componentsin the sample preparation, which would disintegrate or decompose thisspecies without the stabilisation by the nitrogenous compound, is notnecessary or can take place at a later time than usual. It isparticularly preferred if a successive purification of the samplepreparation can be entirely foregone, and the sample preparation can beused directly in an analysis or in a detection method. On the one hand,the detection of the species of nucleic acid or protein is therebyimproved, as this species is present in a stabilised manner in theanalysis solution and its concentration does not decrease in thisanalysis solution or only to a small measure, than with a comparingsystem without nitrogenous compound, and thereby more substance isavailable over the period of the analysis. On the other hand,time-consuming and expensive and contamination-prone purification stepscan be foregone more easily. It was further determined that in thesamples, in which the species of nucleic acid and/or of protein arepresent in addition to cellular substances, as they are particularlypresent in a cell lysate, they can possibly be stabilised additionally.

In a preferred embodiment of the stabilisation method according to theinvention, the sample is a biological sample, which is subjected to alysis and possibly further purification steps prior to the contactingwith the composition for the generation of the fluid sample preparation.The lysis can take place with usual lysis methods, and the furtherpurification steps can for example be a preparation method orimmobilisation method of a nucleic acid or protein preparation.

In a further preferred embodiment of the method according to theinvention, the sample is a biological sample in which the at least onespecies of a nucleic acid and/or at least one protein are contained in acasing, preferably a biological casing, and whereby the sample iscontacted with the fluid or solid composition to produce a lysate. Thesample can also contain organisms. The lysate is preferably generatedfor the lysis of a biological sample according to the method of theinvention described above.

In a further embodiment of the method according to the invention, thesample contains at least two species of the group consisting of nucleicacids and proteins. The sample preparation is generated in such amanner, or the lysis is carried out in such a manner that the two ormore certain species of nucleic acid and/or proteins in the producedsample preparation or the produced lysate, are dissolved or suspended orimmobilised on a carrier material. For example, nucleic acids such asDNA and RNA, in particular gDNA and RNA can be dissolved or suspended inthe sample preparation or in the lysate. Alternatively, proteins canselectively be kept in solution. As described above, during the choiceof the conditions which have to be used with the generation of thesample preparation or the lysis, the type of the sample and thedifferent components, which are contained in the composition used forthe generation of the sample preparation have to be considered, and inparticular the amount of the used nitrogenous compound.

In a further preferred embodiment of the stabilisation method accordingto the invention, the sample contains at least two species from thegroup consisting of nucleic acids and proteins and the samplepreparation or the lysis is carried out in such a manner that thespecies of nucleic acid and/or proteins contained in the sample areessentially dissolved and/or suspended or immobilised in the samplegenerated preparation or the lysate by the majority. Preferably, allspecies are essentially dissolved and/or suspended or immobilised.Thereby, either all of the species of nucleic acids contained in thesample or all of species of proteins contained in the sample can bedissolved and/or suspended. This means, that during the samplepreparation or during the lysis, essentially no precipitation takesplace, as is e.g. used for the removal of nucleic acids or proteins fromlysates. If the sample contains several species of nucleic acids and/orproteins, and two, several or all of these species shall remaindissolved and/or suspended in the lysate after the contacting with thenitrogenous compound, it is particularly preferred that the relativeconcentration of these different species of nucleic acids and/orproteins do not change with regard to one another by the addition of thecomposition containing the nitrogenous compound or through the lysis.That is, the relative concentration of this species in the samplepreparation or the lysate compared to the relative concentration of thisspecies in the untreated sample remains essentially unchanged. It againapplies, as already disclosed above, to consider the type of the sampleand the different possibly used lysis reagants and the type of the usednitrogenous compound during the execution of the lysis and that suitableroutine tests have possibly to be carried out, to determine suitableconditions for a given sample type.

In a further preferred embodiment of the stabilisation method accordingto the invention, DNA and/or RNA are dissolved and/or suspended orimmobilised in the sample preparation or lysate. Additionally oralternatively, at least one species of protein can be dissolved and/orsuspended or immobilised in the sample preparation or in the lysate.

As has already been described above in connection with the methodaccording to the invention for the lysis of a biological sample, thecomposition used for the lysis can contain at least a reagant of thegroup of the complexing agents, detergents, substances for volumerestriction and/or solvents as further lysis reagants. The lysis canalso take place under mechanical action and/or in an enzymatic manner,or the sample can be washed with a hypotonic washing buffer before thelysis. The lysis can thereby be supported by the above-mentioned methodsfor the physical, chemical or enzymatic lysis. Lysis methods withphysical support by heating or homogenisation of the lysate, withchemical support by use of detergents or enzymatic support by use ofproteases as e.g. protease K (if protein is not to be detected),lysozyme or also nucleases (e.g. DNase; in this case DNA cannot bedetected) have proved to be particularly suitable. The implementationsmade above in connection with the lysis method according to theinvention apply here in the same manner.

In the stabilisation method according to the invention, the amount ofthe nitrogenous compound which is added to the sample, is preferablychosen in such a manner that the concentration of the nitrogenouscompound in the produced sample preparation or the lysate is between0.001 mM to 1 M, preferably between 0.001 to 100 mM, particularlypreferably between 0.001 to 30 mM and specially between 0.001 to 19 mMor 0.001 to 15 mM. If polyamines (a) are used, the concentration ispreferably between 0.001 mM and 15 mM, preferably between 0.001 to 1 mM.An essential stabilisation of e.g. RNA is surprisingly determined, evenwith these very small concentrations of polyamines, in particularspermidine. During the use of amino acids (b), the concentration canpreferably be in the region of 0.001 mM to 20 mM, in particular in theregion of 1 to 15 mM. During the use of nitrogenous heterocycles (c),the concentration can preferably be between 0.001 to 20 mM, preferably0.001 to 15 mM. During the use of carboxylic acid amines (e), theconcentration can preferably be between 0.001 to 15 mM. If inorganicammonium compounds are used, the concentration can preferably be between0.001 mM to 100 mM, in particular preferably 0.001 to 15 mM. During theuse of ammonium groups containing inner salt compounds, theconcentration is preferably 0.001 mM to 300 mM, in particular preferably0.001 to 200 mM.

Regarding the type of the nitrogenous compounds, which can preferably beused in the stabilisation method according to the invention, theimplementations made above with regard to the lysis method according tothe invention apply in the same manner.

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of nucleic acid and/orproteins in a sample, whereby the method comprises the following steps:

-   -   providing a sample preparation or a lysate which contains at        least one species of a nucleic acid and/or at least of a        protein, whereby the at least one species of nucleic acid and/or        protein was stabilised with the stabilising method according to        the invention, and    -   use of the sample preparation in a reaction or reaction sequence        suitable for the detection of the at least one nucleic acid or        the at least one protein. The sample preparation is preferably        used directly, without carrying out further method steps for the        reduction of the number of the species of nucleic acids and/or        proteins contained in the sample preparation and/or for the        removal or inactivation of the substances from the sample        preparation effecting the degradation of nucleic acids and/or        proteins.

An improved detection can be achieved by this method, due to thestabilisation of the species of nucleic acid and/or the species ofprotein to be detected, whereby a sample reconditioning preceding thedetection reaction can preferably be foregone. As the species of nucleicacid or protein to be detected is stabilised, the detection can beconducted with small sample amounts.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of nucleic acid and/or protein,the implementations made above in connection with the lysis according tothe invention apply.

In addition to the stabilisation, the use of the nitrogenous compoundduring the generation of the sample preparation or of the lysate canalso lead to a masking of certain further species of nucleic acidcontained in the sample. If the sample is subjected to a lysis, animprovement of the lysis can also be achieved, in particular anincreased concentration of the desired species of nucleic acid and/orprotein in the lysate. In addition to the stabilisation, a masking ofcertain species of nucleic acid can possibly be achieved in the sample.The inhibiting effects in the generated sample preparation or the lysatecan also possibly be decreased by the use of the nitrogenous compound.

In a further aspect, the present invention relates to a method fordecreasing inhibiting effects in a sample, which contains at least aspecies of nucleic acid and/or a species of protein and at least aninhibiting substance. This method comprises the following steps:

-   -   providing a sample which comprises at least one species of a        nucleic acid and/or of a protein, and at least one inhibiting        substance,    -   contacting the sample with a fluid or solid composition to        generate a fluid sample preparation, whereby the composition        contains at least a nitrogenous compound, which is chosen from        the group consisting of a) polyamines, b) amino acids, and        oligo- and polypeptides, c) nitrogenous heterocyclic compounds        including homo or hetero polymers, which comprise these        nitrogenous compounds, d) amines of the type R¹R²NR³, whereby        R¹, R² and R³ are chosen independently from one another from the        group consisting of H, C₁-C₅-alkyl groups and aryl groups,        whereby R¹, R² and R³ are not H simultaneously, e) carboxylic        acid amides, f) inorganic ammonium salts, g) ammonium groups        containing inner salt compounds, h) antibiotica binding nucleic        acid, i) compounds, which bind in the small cavity of the        DNA, j) nitrogenous compounds chosen from the groups described        under a-i with an additional derivation, and mixtures of two or        more of these compounds, whereby the amount of the nitrogenous        compound, which is added to the sample, is chosen in such a        manner that the inhibiting effect of the inhibiting substance is        reduced in the fluid sample preparation.

The term inhibiting substance is to be understood as every substancewhich, in a subsequent analysis or detection method, which is carriedout with the sample preparation or a sample obtained by furtherreconditioning steps, acts in an inhibiting manner, that is, isdisadvantageous for the detection reaction. If nucleic acids are presentin the sample, which are to be detected, e.g. proteins can representsuch inhibiting substances. If proteins are to be detected in thesample, nucleic acids can e.g. represent such inhibiting substances. Themutual inhibiting effect of proteins and nucleic acids can for examplebe based on the formation of nucleoprotein complexes. In preferredembodiments of the present invention, the inhibiting substance is aprotein, in particular a nucleic acid-binding protein, or aprotein-binding nucleic acid.

An interaction between the species of nucleic acid and/or the species ofprotein and the inhibiting substance takes place which affects ananalysis or detection reaction carried out with the sample preparationin a disadvantageous manner is understood to be an inhibiting effecthere. By the presence of the inhibiting substance, the result of thisreaction with regard to an identical sample which does not contain theinhibiting substance, is thereby influenced in a disadvantageous manner.A reduction of the inhibiting effect can be determined in that e.g. afollowing analysis or detection reaction of a certain species of nucleicacid or protein, which is carried out with a sample, to which was addedone of the nitrogenous compounds which are used according to theinvention, is improved compared to the same analysis or detectionreaction which was carried out with the same sample, to which nonitrogenous compound was added.

A sample is, in addition to organisms, which are subjected to a lysisfor the purpose of the disintegration, every mixture of materials whichcomprises at least one species of a nucleic acid and/or of a protein.This can be a mixture of materials or only the pure nucleic acid or theprotein. These mixtures of material can be obtained e.g. through nucleicacid or protein acid preparations. The sample can thereby be present asa solid or as a solution, or it can be pure organisms or suspensions oforganisms in a fluid medium as e.g. cell cultures. The composition ofthe sample can be added as a fluid, e.g. as a buffer solution or as asolid in dependence of the type of the sample.

In a preferred embodiment of the present invention, the sample is abiological sample, which is subjected to a lysis and possibly furtherpurification steps prior to the contacting with the composition for thegeneration of the fluid sample preparation. The lysis can take placewith usual lysis methods, and the further purification steps can forexample be a preparation method of a nucleic acid or proteinpreparation. The lysis can thereby be supported by the above-mentionedmethods for the physical, chemical or enzymatic lysis. Lysis methodswith physical support by heating or homogenisation of the lysate, withchemical support by use of detergents or enzymatic support by use ofproteases as e.g. protease K (if protein is not to be detected),lysozyme or also nucleases (e.g. DNase; in this case DNA not detected)have proved to be suitable.

In an embodiment of this method, the stabilisation of nucleic acids iscarried out by one of the chosen substances following an enzymatic,physical or chemical lysis, in particularly preferred using detergentsand protease as e.g. proteinase K. Thus, detergents with a concentrationof 0.005 to 10% are used for example. Proteases as e.g. the proteinase Kcan be contained in the stabilised sample in a concentration of 0.5×10⁻⁴mAU/μl to 50×10⁻⁴ mAU/μl.

In a further embodiment of this method, the stabilisation of RNA by oneor more of the claimed substances is carried out following an enzymaticdegradation by an endonuclease as e.g. DNase. The DNase I can thus becontained in a concentration of 0.003 U/μl to 0.5 U/μl in the stabilisedsample.

In a further embodiment of this method, the stabilisation of protein byone or more of the claimed substances is carried out following anenzymatic degradation by nucleic acids by nucleases as e.g. RNase,DNases, benzonases etc.

In a further embodiment of this method, the stabilisation ofbiomolecules is carried out in the sample e.g. of nucleic acid orprotein by one or several of the claimed substances chosen from e.g.arginine, imidazole, proline, lysine, spermine, spermidine, glutamicacid, indazole, thymine, thymidine, guanine, guanosine, adenine,histidine, tryptophane, ammonium sulfate or by a mixture of these.

In a further preferred embodiment of this aspect of the presentinvention, the at least one species of nucleic acid or protein isimmobilised on a carrier material before or during the addition of thenitrogenous compound. The carrier materials described already inconnection with other aspects of the present invention can again be usedthereby.

In a further preferred embodiment of this method according to theinvention, the sample preparation is carried out in such a manner thatthe at least one species of the nucleic acid and/or of the protein isdissolved and/or suspended in the fluid sample preparation. This canparticularly be effected by the addition of suitable amounts of thenitrogenous compound to the sample. If a lysis of a biological sample iseffected by the addition of the composition, the lysis cancorrespondingly be carried out in such a manner that at least onespecies of the nucleic acid/and or of the protein is dissolved and/orsuspended in the fluid sample preparation.

In a further preferred embodiment of the method according to theinvention, the sample is a biological sample in which the at least onespecies of a nucleic acid and/or at least of a protein is contained in acasing, e.g. a biological casing, and whereby the sample is contactedwith the fluid or solid composition to produce a lysate. The sample canalso contain organisms. The lysate is preferably generated for the lysisof a biological sample according to the method according to theinvention described above.

As already described above in the stabilisation method according to theinvention, the sample contains, in a preferred embodiment of the methodaccording to the invention, at least two species from the groupconsisting of nucleic acids and proteins for the decrease of inhibitingeffects, and the generation of the sample preparation or the lysis iscarried out in such a manner that a plurality of the species of nucleicacid and/or proteins contained in the sample are dissolved and/orsuspended or immobilised in the sample preparation or the lysate.Preferably, essentially all of these species are dissolved and/orsuspended or immobilised in a variant of the method. Thereby, either allof the species of nucleic acids contained in the sample or all of thespecies of proteins contained in the solution can be dissolved and/orsuspended or immobilised. The implementations made above in connectionwith the analog embodiment of the stabilisation method apply here in thesame manner.

This means that essentially no precipitation takes place during thegeneration of the sample preparation or the lysis, as is used e.g. forthe removal of nucleic acids or proteins from lysates. If the samplecontains several species of nucleic acid and/or proteins, and two,several or all of these species shall remain dissolved and/or suspendedin the lysate after the lysis, it is particularly preferred that therelative concentration of these different species of nucleic acidsand/or proteins do not change with regard to one another by the lysisand thereby the relative concentration of these species in the lysateremains essentially unchanged with regard to the relative concentrationof this species in the sample. It again applies, as already disclosedabove, to consider the type of the sample and the different possiblyused lysis reagants and the type of the used nitrogenous compound duringthe execution of the lysis and that suitable routine tests have possiblyto be carried out, to determine suitable conditions for a given sampletype. Suitable routine tests have to be carried out if necessary, so asto determine suitable conditions for a given sample type.

In the method according to the invention for decreasing inhibitingeffects, a preferred embodiment provides that DNA and/or RNA iscontained in the lysate, in particular dissolved and/or suspended.Additionally or alternatively, at least one species of protein can becontained in the lysate, in particular be dissolved or suspended.

As has already been described above in connection with the methodaccording to the invention for the lysis of a biological sample, thecomposition used for the lysis can contain at least a reagant of thegroup of the complexing agents, detergents, substances for volumerestriction and/or solvents as further lysis reagants. The lysis canalso take place under mechanical action and/or in an enzymatic manner,or the sample can be washed with a hypotonic washing buffer before thelysis. The implementations made above in connection with the lysismethod according to the invention apply here in the same manner.

In the stabilisation method according to the invention, the amount ofthe nitrogenous compound which is added to the sample, is preferablychosen in such a manner that the concentration of the nitrogenouscompound in the produced sample preparation or the lysate is between0.001 mM to 1 M, preferably between 0.001 to 100 mM, particularlypreferably between 0.001 to 50 mM or 0.001 to 30 mM and specially 0.001to 10 mM. If polyamines (a) are used, the concentration is preferablybetween 0.001 mM and 15 mM, preferably between 0.001 to 1 mM. During theuse of amino acids (b), the concentration can preferably be in theregion of 0.001 mM to 20 mM, in particular in the region of 1 to 15 mM.During the use of nitrogenous heterocycles (c), the concentration canpreferably be between 0.001 to 50 mM, preferably 0.001 to 30 mM. Duringthe use of carboxylic acid amines, (e), the concentration can preferablybe between 0.001 to 20 mM. If inorganic ammonium compounds are used, theconcentration can preferably be between 0.001 mM to 100 mM, inparticular preferably from 0.001 to 50 mM. During the use of antibioticabinding nucleic acid, the concentration can preferably be 0.001 to 15mM, in particular preferably 0.001 to 1 mM.

In a particularly preferred embodiment of the method according to theinvention for the decrease of inhibiting effects, the at least onenucleic acid species is a DNA species, in particular gDNA and/or a RNAspecies.

Regarding the type of the nitrogenous compounds, which can preferably beused in the method according to the invention for reducing inhibitingeffects, the implementations made above with regard to the lysis methodaccording to the invention or the stabilisation method according to theinvention apply in the same manner.

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of nucleic acid and/orproteins in a sample, whereby the method comprises the following steps:a) providing a sample preparation or a lysate, according to theinvention, which contains at least one species of a nucleic acid and/orat least of a protein, whereby the sample preparation or the lysate weredecreased with at least one inhibiting effect with the method accordingto the invention for decreasing inhibiting effects;

b) use of the sample preparation in a reaction or reaction sequencesuitable for the detection of the at least one nucleic acid or the atleast one protein.

By this method, due to the decrease of the inhibiting effects in thesample preparation or the lysate, an improved detection of the speciesto be analysed can be achieved, whereby a sample reconditioningpreceding the detection reaction for the separation of the inhibitingsubstance can be foregone.

In a preferred embodiment of this analysis method according to theinvention, the sample preparation or the lysate in step b) iscorrespondingly used directly, without carrying out further method stepsfor the reduction of the number of species of nucleic acid and/orproteins contained in the sample preparation or that further steps forthe removal of substances, which effect the degradation of nucleic acidsand/or proteins have to be carried out from the sample preparation, orthat such substances have to be inactivated. The sample preparation orthe lysate is thereby preferably used directly for the analysis or forthe production of a reaction solution suitable for the analysis, withoutany further reconditioning step.

In a further embodiment, the lysis can be supported by theabove-mentioned methods for the physical, chemical or enzymatic lysis.In particular, lysis methods with physical support by heating orhomogenisation of the lysate, with chemical support by the use ofdetergents or enzymatic support by the use of proteases as e.g. proteaseK (if protein is not to be detected), lysozyme or also nucleases (e.g.DNase; in this case DNA cannot be detected) have proved to be suitable.

In an embodiment of this method, the stabilisation of nucleic acid byone of the chosen substances is carried out following an enzymatic,physical or chemical lysis, in particularly preferred using detergentsand protease as e.g. proteinase K. Thus, detergents with a concentrationof 0.005 to 10% are e.g. used. Proteases as e.g. the proteinase K can becontained in the stabilised sample in a concentration of 0.5×10⁻⁴ mAU/μlto 50×10⁻⁴ mAU/μl.

In a further embodiment of this method, the decrease of the inhibitingeffect is carried out by one or more of the claimed substances. Anucleic acid degradation can in particular be improved by one of thesubstances. The DNase I can thus degrade DNA in a concentration of 0.003to 0.5 U/μl in the sample.

In a further embodiment of this method, the stabilisation ofbiomolecules is carried out in the sample e.g. of nucleic acid orprotein by one or several of the claimed substances chosen from e.g.treatment of the at least two species of biomolecule is carried out inthe sample through a substance chosen from e.g. arginine, imidazole,proline, lysine, spermine, spermidine, glutamic acid, indazole, thymine,thymidine, guanine, guanosine, adenine, histidine, tryptophane, ammoniumsulfate or by a mixture of these.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of nucleic acid and/or protein,the implementations made above with regard in connection with the lysisaccording to the invention apply here.

In a particularly preferred embodiment of this analysis method accordingto the invention, the sample preparation or the lysate contains RNA inaddition to gDNA and the reaction sequence in step b) optionallycomprises the reaction of nucleic acids with enzymes. These reactionscan be in particular: b1) optional degradation of gDNA and successivelyb2) RT-PCR, preferably real-time RT-PCR for the detection of RNA. Thelysate can alternatively contain RNA in addition to gDNA and thereaction or the reaction sequence in step b) comprises the followingsteps: b1) PCR, preferably real-time RT-PCR for the detection of gDNA orb2) RT-PCR, preferably real-time RT-PCR for the detection of RNA. ThePCR or RT-PCR can thereby optionally proceed as end point, as multiplexand/or as real-time reaction.

In one embodiment of the method according to the invention, a firstconversion product of a chosen nucleic acid is provided with theanalysis method, e.g. first strand cDNA from RNA.

Regarding the above explained method for decreasing of inhibitingeffects in a sample, the nitrogenous compound contained in the samplepreparation or the lysate can also lead to an additionally improvedlysis, a stabilisation of certain species of nucleic acid and/orproteins and to a masking of certain nucleic acids.

In a further aspect, the present invention relates to a method for theselective masking of at least one species of a nucleic acid in a sample,which contains at least one first species of a nucleic acid and a secondspecies different to the first species. This method comprises thefollowing steps:

-   -   providing a sample which contains at least two different species        of nucleic acid, contacting the sample with a fluid or solid        composition to produce a fluid sample preparation, whereby the        composition contains at least a nitrogenous compound, which is        selected from the group consisting of:        -   polyamines, b) amino acids and oligo and und polypeptide, c)            nitrogenous heterocyclischic compounds, including homo or            heteropolymeres, which comprise these nitrogenous            compounds, d) amines of the type R¹R²NR³, whereby R¹, R² and            R³ are chosen different from one another from the group            consisting of H, C₁-C₅-alkyl groups and aryl groups, whereby            R¹, R² and R³ are not H simultaneously, e) carboxylic acid            amides, f) inorganic ammonium salts, g) ammonium groups            containing inner salt compounds, h) antibiotica binding            nucleic acid, i) compounds, which bind in the small cavity            of the DNA, j) nitrogenous compounds chosen from the groups            described under a-i with an additional derivation, and            mixtures of two or more of these compounds, whereby the            generation of the sample preparation is carried out in such            a manner that a first and a second species of nucleic acid            is dissolved and/or suspended in the fluid sample            preparation and whereby the amount of the nitrogenous            compound is chosen in such a manner, that the second species            of nucleic acid is masked in such a manner that the first            species of nucleic acid can be detected in an improved            manner in a detection method for nucleic acids, compared to            the same detection method, where the nitrogenous compound            was not added to the sample.

A simple differential analysis of the second species of nucleic acid inthe sample is enabled by this method. In this method, the first speciesof nucleic acid, which cannot be analysed in the differential analysis,but which potentially could disturb or falsify the detection reaction ofthe second species, can be systematically masked in the sample. Aseparation of the first or second species of nucleic acid from thesample can thereby be foregone.

In other words, the differential analysis of DNA and RNA results e.g. ina differential masking of DNA or RNA, so that the masked nucleic acidcannot be detected within the analysis or with low efficiency, or doesnot influence the result of the analysis of the second species in anegative manner.

In preferred embodiments of the masking method according to theinvention, the sample is a biological sample, which is subjected to alysis and possibly further purification steps prior to the contactingwith the composition for the generation of the fluid sample preparationof a lysis. In a further preferred embodiment, the sample is abiological sample in which the species of nucleic acids are contained ina casing, preferably a biological casing, and whereby the sample iscontacted with the fluid or solid composition to produce a lysate. In afurther preferred embodiment, the sample contains at least two speciesof nucleic acid and the generation of the sample preparation or thelysis is carried out in such a manner that several certain species ofnucleic acid and/or proteins are dissolved or suspended in the generatedlysate. It is further preferred that the sample contains at least twospecies of nucleic acid and the generation of the sample preparation orthe lysis is carried out in such a manner that essentially all or aplurality of the species of nucleic acid contained in the sample aredissolved and/or suspended in the sample preparation or in the lysate.It is further preferred that the composition which contains thenitrogenous compound, contains at least a reagant of the group of thecomplexing agents, detergents, substances for volume restriction and/orsolvents as further lysis reagents. The lysis can also take place undermechanical action and/or in an enzymatic manner, or the sample can bewashed with a hypotonic washing buffer before the lysis. Regarding allthese preferred embodiments, the embodiments made above in connectionwith the lysis method according to the invention and the stabilisationmethod according to the invention or the method according to theinvention for the reduction of inhibiting effects apply.

In further preferred embodiments of the method according to theinvention for the selective masking is:

-   -   the first species of nucleic acid and the second species of        nucleic acid a species of RNA or PNA; or    -   the first species of nucleic acid is a species of RNA and the        second species of nucleic acid is a species of DNA; or    -   the first species of nucleic acid is a species of PNA and the        second species is a species of DNA or RNA,    -   the first species of nucleic acid and the second species of        nucleic acid are a species of DNA, or

c) the first species of nucleic acid and the second species of nucleicacid are a species of RNA, or

e) the first species of nucleic acid and the second species of nucleicacid are nucleic acid PNA.

In preferred embodiments of the method according to the invention forthe selective masking, the amount of the nitrogenous compound in thegeneration of the sample preparation or the lysate in such a manner thatthe concentration of the nitrogenous compound in the generated samplepreparation or the lysate is between 0.001 mM to 1 M, preferably 0.001mM to 100 mM, in particular preferably 0.001 to 30 mM, especially 0.001to 19 mM or 0.001 to 15 mM. During the use of polyamines (a), inparticular spermidine for the selective masking of DNA, e.g. gDNA,preferably compared to RNA, the concentration is preferably 0.001 to 10mM, preferably 0.001 to 1 mM. During the use of amino acids (b) for theselective masking of DNA, e.g. gDNA, preferably compared to RNA, theconcentration can preferably be 0.001 to 50 mM, in particular preferably0.001 to 30 mM. During the use of nitrogenous heterocyclic compounds forthe masking of DNA, e.g. gDNA, preferably compared to RNA, theconcentration can preferably be 0.001 to 30 mM, preferably 0.001 to 20mM. During the use of anporganic ammonium compounds for the masking ofDNA, e.g. gDNA, preferably compared to RNA, the concentration canpreferably be 0.001 to 50 mM, preferably 0.001 to 30 mM. During the useof carboxylic acid amides for the masking of DNA, e.g. gDNA, preferablycompared to RNA, the concentration can preferably be 0.001 to 20 mM,preferably 0.001 to 10 mM. The concentration to be chosen can beinfluenced by the type of the sample and has possibly to be consideredas well.

Regarding the type of the nitrogenous compounds, which can preferably beused in the method according to the invention for reducing inhibitingeffects, the implementations made above with regard to the lysis methodapply in the same manner.

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of nucleic acid and/orproteins in a sample, whereby the method comprises the following steps:

-   -   providing a sample preparation which contains at least a first        species of nucleic acid and a second species of nucleic acid,        and whereby the first species of nucleic acid is different from        the second species of nucleic acid, whereby the first species of        nucleic acid was masked with the method for the selective        masking according to the invention and    -   use of the sample preparation or the lysate in a reaction or        reaction sequence suitable for the detection of the second        nucleic acid.

The analysis method according to the invention can be carried out by theselective masking without a previous separation of the possibly theanalysis of a second species of nucleic acid influencing the firstspecies of nucleic acid in a disadvantageous manner. The analysis methodis improved and simplified thereby, elaborate separation steps to becarried out before the analysis can be omitted.

In a preferred embodiment of the analysis method according to theinvention, step b) is carried out without carrying out further methodsteps for the reduction of the number of species of nucleic acidcontained in the sample preparation and/or without further steps for theremoval of materials from the sample preparation which effect thedegradation of nucleic acids or without further method steps for theinactivation of those substances in the sample preparation. The samplepreparation or the lysate is preferably used directly without a furtherreconditioning step in the reaction or the reaction sequence for thedetection of the second nucleic acid species or for the production of areaction solution suitable for the analysis. The sample preparation forthe detection of a certain species of nucleic acid is therebyconsiderably simplified, whereby the expenditure of time and the costsand error susceptibility of the analysis method can be reduced.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of nucleic acid, theimplementations made above in connection with the previously describedaspects of the present invention, e.g. the lysis according to theinvention, apply.

In a particularly preferred embodiment of the differential analysismethod, the reaction or reaction sequence used in step b) for thedetection of the second species of nucleic acid is a PCR or RT-PCR,preferably a real-time PCR or real-time RT-PCR. Preferably, the firstspecies of nucleic acid is gDNA and the second species of nucleic acidis RNA in the sample preparation or in the lysate, and in step b) thereaction or the reaction sequence is a RT-PCR, preferably a real-timeRT-PCR. There, the nitrogenous compound selected from the group of thepolyamines, heterocycles, amino acids, carboxylic acid amides andammonium compounds described above with regard to the lysis methodaccording to the invention, preferably compounds selected from the groupconsisting of spermidine, ammonium sulfate, ammonium hydrogen phosphate,glycine, 2,3-dimethylpyrazine, benzimidazole, imidazole, arginine,histidine, urea and distamycine, in particular distamycine D.

In a further preferred embodiment of the differential analysis methodaccording to the invention, the first species of nucleic acid RNA andthe second species of nucleic acid is DANN, preferably gDNA in thesample preparation or in the lysate. In step b), the reaction or thereaction sequence is a RT-PCR, preferably a real-time RT-PCR.Preferably, the compound described here in connection with the lysismethod according to the invention selected from the group of theheterocycles, amino acids and ammonium compounds are used here, which aparticularly selected from the group consisting of proline, indazole andammonium sulfate.

The present invention will be explained in more detail in the followingwith chosen examples and the corresponding figures. The examples servethe purpose of the clarification of the present invention and are not tobe seen as restricting.

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of DNA in a sample, wherebythe method comprises the steps:

-   -   providing a sample preparation or a lysate, which contains at        least one species of a RNA, whereby the at least one species of        RNA was treated with at least one of the substances in a sample        preparation according to the invention, and    -   use of the sample preparation in a reaction or reaction sequence        suitable for the detection of the at least one species of RNA.        The sample preparation is preferably used directly, without        carrying out further method steps for the reduction of the        number of the species of nucleic acids and/or proteins contained        in the sample preparation and/or for the removal or inactivation        of the substances from the sample preparation effecting the        degradation of nucleic acids and/or proteins.

In one embodiment of this method, the treatment of the at least onespecies of RNA is carried out by one of the chosen substances, when theRNA is contained in organisms, in particular in single cells, cellassemblies, tissues or whole animals or plants, cultivated cells, orexcretion products or secretions as e.g. stabilised and non-stabilisedblood, plasma, serum, tissue fluids, sperm, swabs, sputum, saliva, tearfluid, urine, excrements, hair, danders, bacteria, viruses etc.

In one embodiment of the method according to the invention, theabove-mentioned organisms can be pretreated with a washing solutionbefore the treatment with the substances according to the invention.Particularly preferred, a washing solution is used which removescontaminations and/or prepares the sample for the treatment with thesubstances according to the invention in another manner.

By this method, an improved detection and/or a reaction can be achieveddue to the treatment of the species of RNA to be detected.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of RNA, the implementations madeabove in connection with the lysis according to the invention apply.

In a further embodiment of the method according to the invention, theorganisms are incubated with the lysis buffer, preferably between 1 to120 minutes. In a further embodiment of the method according to theinvention, the organisms are incubated with the lysis buffer at atemperature which is increased compared to room temperature, preferablyat 30 to 90° C., particularly preferably at 50 to 85° C.

In a further embodiment of this method, the treatment of the at leastone species RNA is carried out by one of the chosen substances, duringor after an enzymatic, physical or chemical lysis, in particularpreferred using detergents and protease as e.g. proteinase K. Thus,detergents with a concentration of 0.005 to 10% are used for example.Proteases as e.g. the proteinase K can be contained in the stabilisedsample in a concentration of 0.5×10⁻⁴ mAU/μl to 50×10⁻⁴ mAU/μl.

In a further embodiment of this method, the treatment of the at leastone species RNA is carried out by one of the chosen substances during orafter an enzymatic degradation of DNA by an endonuclease as e.g. DNase.The DNase I can thus be contained in the stabilised sample in aconcentration of 0.003 U/μl to 0.5 u/μl.

In a further embodiment of the method according to the invention, theenzymes are deactivated after an enzymatic treatment, for example byincreasing the temperature, for example to 60 to 95° C.

In a further embodiment of this method, the treatment of the at leastone species of RNA is carried out by one of the chosen substances and aphysical treatment step, in particular preferred by shear forces,pressure differences or temperature influence.

In a further embodiment of this method, the treatment of the at leastone species of RNA is carried out in the sample by one or more of theclaimed substances chosen from e.g. arginine, imidazole, proline,lysine, spermine, spermidine, glutamic acid, indazole, thymine,thymidine, guanine, guanosine, adenine, histidine, tryptophane, ammoniumsulfate or by a mixture of these.

In a further embodiment of this method, the treatment of the at leastone species of RNA is carried out in a solution which contains at leastone of the described substances, whereby the solution comprises a pHbetween 7.1 and 14, preferably a pH between 7.1 and 12, and especiallypreferably a pH between 7.4 and 10.

The reaction or reaction sequence suitable for the detection of the atleast one species of RNA can thereby e.g. be selected from the group ofthe nucleic acid binding reactions, in particular the nucleic acidhybridisations, in particular polymerisations of nucleic acids and inparticular the group of the amplification reactions. In a particularembodiment of this method, the detection method of the at least onespecies of RNA is a PCR (polymerase chain reaction), real-time-PCR (asprobe-based method and as a method which depends on asequence-unspecific binding detector molecule as e.g. SybrGreen), RT-PCR(reverse transcription polymerase chain reaction), Real-time-RT-PCR (asprobe-based method and as a method which depends on asequence-unspecific binding detector molecule as e.g. SybrGreen),multiplex PCR, multiplex RT-PCR, the probe-based methods of thereal-time multiplex PCR and real-time multiplex RT-PCR. The term RT-PCRin the described connection is to be understood as follows: The reactionof the RT-PCT consists of a reverse transcription and a PCR, wherebyboth reactions can take place independently from one another in twoseparate containers or together in one container. Both reactions can becarried out by one or more enzymes. In addition to the RT-PCR, otherreactions can also be carried out with the at least one species of RNAas e.g. NASBA (nucleic acid sequence based amplification), 3SR (sequencesustained self replication). 2SR, TMA (transcription mediatedamplification), MDA (multiple displacement amplification), rollingcircle amplification, whole-transcriptome-amplification,whole-genome-amplification and rolling transcription amplification orloop-mediated isothermal amplification (LAMP).

In a further aspect, the present invention relates to an analysis methodfor the detection of at least one species of DNA in a sample, wherebythe method comprises the steps:

-   -   providing a sample preparation or a lysate which contains at        least one species of a DNA, whereby the at least one species of        DNA was treated with at least one of the substances according to        the invention in a sample preparation, and    -   use of the sample preparation in a reaction or reaction sequence        suitable for the detection of the at least one species of a DNA.        The sample preparation is preferably used directly, without        carrying out further method steps for the reduction of the        number of the species of nucleic acids and/or proteins contained        in the sample preparation before the detection reaction and/or        for the removal or inactivation of the substances from the        sample preparation effecting the degradation of nucleic acid        and/or proteins.

In one embodiment of this method, the treatment of the at least onespecies of DNA is carried out by one of the chosen substances, when theDNA is contained in organisms, in particular in single cells, cellassemblies, tissues or whole animals or plants, cultivated cells, orexcretion products or secretions as e.g. stabilised and non-stabilisedblood, plasma, serum, tissue fluids, sperm, swabs, sputum, saliva, tearfluid, urine, excrements, hair, danders, bacteria, viruses etc.

In one embodiment of the method according to the invention, theabove-mentioned organisms can be pretreated with a washing solutionbefore the treatment with the substances according to the invention.Particularly preferred, a washing solution is used which removescontaminations and/or prepares the sample for the treatment with thesubstances according to the invention in another manner.

By this method, an improved detection and/or reaction can be achieveddue to the treatment of the species of DNA to be detected.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of DNA, the implementations madeabove in connection with the lysis according to the invention apply.

In a further embodiment of the method according to the invention, theorganisms are incubated with the lysis buffer, preferably between 1 to120 minutes. In a further embodiment of the method according to theinvention, the organisms are incubated with the lysis buffer at atemperature which is increased compared to room temperature, preferablyat 30 to 100° C., particularly preferably at 50 to 85° C.

In a further embodiment of this method, the treatment of the at leastone species DNA is carried out by one of the chosen substances carriedout before, during or after an enzymatic, physical or chemical lysis, inparticular preferred using detergents and protease as e.g. proteinase K.Thus, detergents with a concentration of 0.005 to 10% are used.Proteases as e.g. the proteinase K can be contained in the stabilisedsample in a concentration of 0.5×10⁻⁴ mAU/μl to 50×10⁻⁴ mAU/μl.

In a further embodiment of this method, the treatment of the at leastone species DNA is carried out by one of the chosen substancessubsequent to an enzymatic degradation of RNA by an endonuclease as e.g.RNase.

In a further embodiment of the method according to the invention, theenzymes are deactivated after an enzymatic treatment, for example byincreasing the temperature, for example to 60 to 100° C.

In a further embodiment of this method, the treatment of the at leastone species of DNA in the sample is carried out by a substance chosen ofe.g. tryptophane, proline, histidine or guanosine or by a mixture ofthese.

In a further embodiment of this method, the treatment of the at leastone species of DNA is carried out in a solution which contains at leastone of the described substances, whereby the solution comprises a pHbetween 7.1 and 14, preferably a pH between 7.1 and 12, and especiallypreferably a pH between 7.4 and 10.

In a further embodiment of this method, the treatment of the at leastone species of DNA is carried out through one of the chosen substancesand a physical treatment step, particularly preferred by temperatureinfluence.

The reaction or reaction sequence suitable for the detection of the atleast one species of DNA can thereby be selected from e.g. the group ofthe nucleic acid binding reactions, in particular the nucleic acidhybridisations, in particular polymerisations of nucleic acids and inparticular of the group of the amplification reactions. In a particularembodiment of this method, the detection method of the at least onespecies of RNA is a PCR (polymerase chain reaction), real-time-PCR (asprobe-based method and as a method which depends on asequence-unspecific binding detector molecule as e.g. SybrGreen),multiplex PCR, multiplex RT-PCR, the probe-based methods of thereal-time multiplex PCR and real-time multiplex RT-PCR. In addition tothe PCR, other reactions can also be carried out with the at least onespecies of DNA as e.g. MDA (multiple displacement amplification),rolling circle amplification, whole-genome-amplification and rollingtranscription amplification or loop-mediated isothermal amplification(LAMP).

In a further aspect, the present invention relates to an analysis methodfor the detection of at least two species of biomolecules, for exampleat least one species of a nucleic acid and at least one species of aprotein in a sample, whereby the method comprises the following steps:

-   -   providing a sample preparation or a lysate which contains at        least two species of biomolecules, for example at least one        species of a nucleic acid and at least one species of a protein,        whereby the at least one species of nucleic acid and/or protein        was treated with at least one of the substances according to the        invention, and    -   use of the sample preparation in a reaction or reaction sequence        suitable for the detection of at least two species of        biomolecules, for example at least one species of a nucleic acid        and one species of protein. The sample preparation is preferably        used directly, without carrying out further method steps for the        reduction of the number of the species of nucleic acids and/or        proteins contained in the sample preparation and/or for the        removal or inactivation of the substances from the sample        preparation effecting the degradation of nucleic acids and/or        proteins.

In one embodiment of this method, the treatment of nucleic acids and/orproteins is carried out by one of the chosen substances, when thenucleic acid and/or protein is contained in organisms, in particular insingle cells, cell assemblies, tissues or whole animals or plants,cultivated cells, or excretion products or secretions as e.g. stabilisedand non-stabilised blood, plasma, serum, tissue fluids, sperm, swabs,sputum, saliva, tear fluid, urine, excrements, hair, danders, bacteria,viruses etc.

In one embodiment of the method according to the invention, theabove-mentioned organisms can be pretreated with a washing solutionbefore the treatment with the substances according to the invention.Particularly preferred, a washing solution is used which removescontaminations and/or prepares the sample in another mariner for thetreatment with the substances according to the invention.

By this method, nucleic acids and/or proteins can be detected likewisein a reaction due to the treatment in a treated sample.

By this method, RNA and DNA or RNA and proteins or DNA and proteins canbe detected due to the treatment in a treated sample.

Regarding the type of the reaction or reaction sequence used for thedetection of the corresponding species of nucleic acid and/or protein,the implementations made above in connection with the lysis according tothe invention apply.

In one embodiment of this method for the detection of RNA and DNA in atreated sample, the treatment of the nucleic acids with one of thechosen substances is carried out before, during or after an enzymatic,physical or chemical lysis, in particular preferred using detergents andprotease as e.g. proteinase K. Thus, detergents with a concentration of0.005 to 10% are e.g. used. Proteases such as e.g. the proteinase K canbe contained in the stabilised sample in a concentration of 0.5×10⁻⁴mAU/μl to 50×10⁻⁴ mAU/μll.

In one embodiment of this method for the detection of RNA and protein ina treated sample, the treatment of the nucleic acids with one of thechosen substances is carried out before, during or after an enzymatic,physical or chemical lysis, in particular preferred using detergentsand/or DNA-specific nuclease. Thus the DNase I can be contained in thestabilised sample in a concentration of 0.003 U/μl to 0.5 U/μl.

In one embodiment of this method for the detection of DNA and protein ina treated sample, the treatment of the nucleic acids with one of thechosen substances is carried out before, during or after an enzymatic,physical or chemical lysis, in particular preferred using detergentsand/or RNA-specific nuclease.

In a further embodiment of the method according to the invention, theorganisms are incubated with the lysis buffer, preferably between 1 to120 minutes. In a further embodiment of the method according to theinvention, the organisms are incubated with the lysis buffer at atemperature which is increased compared to room temperature, preferablyat 30 to 85° C. particularly preferably at 50 to 80° C.

In a further embodiment of this method, the treatment of the at leasttwo species of biomolecule is carried out in the sample through asubstance chosen from e.g. arginine, proline, or imidazole or a mixtureof these.

In a further embodiment of this method, the treatment of the sample iscarried out in a solution which contains at least one of the describedsubstances, whereby the solution comprises a pH between 7.1 and 14,preferably a pH between 7.1 and 12, and especially preferably a pHbetween 7.4 and 10.

Thereby, the reaction or reaction sequence suitable for the detection ofthe at least one species of nucleic acid can be selected from the groupof the nucleic acid binding reactions, in particular the nucleic acidhybridisations, in particular polymerisations of nucleic acids and inparticular of the group amplification reactions. In a particularembodiment of this method, the detection method of the at least onespecies of RNA is a PCR (polymerase chain reaction), real-time PCR (asprobe-based method and as a method which depends on asequence-unspecific binding detector molecule as e.g. SybrGreen), RT-PCR(reverse transcription polymerase chain reaction), Real-time-RT-PCR (asprobe-based method and as a method which depends on asequence-unspecific binding detector molecule as e.g. SybrGreen),multiplex PCR, multiplex RT-PCR, the probe-based methods of thereal-time multiplex PCR and real-time multiplex RT-PCR. The term RT-PCRis to be understood as follows in the described connection: The reactionof the RT-PCR consists of a reverse transcription and a PCR, wherebyboth reactions can take place independently from each other in twoseparate containers or together in one container. Both reactions can becarried out by one or more enzymes. In addition to the RT-PCR, otherreactions can also be carried out with the at least one species of RNAas e.g. NASBA (nucleic acid sequence based amplification), 3SR (sequencesustained self replication), 2SR, TMA (transcription mediatedamplification), MDA (multiple displacement amplification) rolling circleamplification, whole-transcriptome-amplification,whole-genome-amplification and rolling transcription amplification orloop-mediated isothermal amplification (LAMP).

The reaction or reaction sequence suitable for the detection of the atleast one protein is selected from the group of the protein bindingreactions, in particular protein recognition, in particular by otherproteins, reactions based on the enzymatic activity of the protein,antibodies, aptameres, ligands, nucleic acids, in particular Westernblotting, or other substances such as gluathione and NAD, or is selectedfrom the group of the protein modification or processing, in particular(de)phosphorylation, (de)glycolysation and splitting through proteases.

All methods mentioned above can be carried out either in solution,suspension or solid phase.

EXAMPLES

In the following examples, the nitrogenous compounds as defined in thepresent invention in the claims are called additive.

Insofar it is not described otherwise in the following, the followingmaterials were used in the examples:

Parent Solutions:

-   -   500 mM EGTA, pH 8    -   500 mM EGTA, pH 8    -   TE-Buffer, 10 mM Tris-HCl, 1 mM EDTA, pH 7.5    -   EPE: 0.06 vol-% Nonidet P40, 1 mM EDTA, 1 mM EGTA, 0.1 vol-%        polyethylene glycol MG 6000 (PEG)

Devices:

ABI Prism 7700 (ABI, Foster City, Calif., USA) (Real-time-RT-PCR)

PCR-ThermoCycler (Biometra GmbH, Gottingen, Germany)

Spectrophotometer for determining the concentration of DNA or RNA(Beckman DU 7400,

Beckman Coulter Inc., Fullerton, Calif., USA)

Agilent Bioanalyzer (Agilent, USA) (denatured gel analysis)

Cell Cultures:

HeLa cells

293 cells

HUH 7 cells

NIN3T3 cells

HepG2 cells

MCF7 cells

Media:

D-MEM (BRL; USA) partially with the additives 10% FCS, 1% Pen/Streptand/or 1% non-essential amino acids for the cells Hela, HUH7, 293,NIH3T3

RPMI 1640 (BRL; USA) partially with the additives 10% FCS, 1% glutamineand/or 1% PEN/Strept for HepG2 cells

RPMI 1640 (BRL; USA) partially with the additives 10% FCS, 1% sodiumpyruvate, 1% glutamine, 1% Pen/Strept, 1% non-essential AS and/or 0.25%bovine insulin for MCF7 cells

Kits and Enzymes:

RNeasy®: RNA preparation method of QIAGEN GmbH, Hilden, Germany

RNeasy 96®: RNA preparation method of QIAGEN GmbH, Hilden, Germany

Omniscript® RT-Kit: Kit for the reverse transcriptase reaction of RNA(QIAGEN GmbH, Hilden, Germany)

Sensicript® RT-Kit: Kit for the reverse transcriptase reaction of RNA(QIAGEN GmbH, Hilden, Germany)

QuantiTect® SybrGreen PCR Kit: Kit for the real-time PCR with SybrGreen(QIAGEN GmbH, Hilden, Germany)

QuantiTect® sample PCR Kit: Kit for the real-time PCR with marked probes(QIAGEN GmbH, Hilden, Germany)

DNase I: (QIAGEN GmbH, Hilden, Germany)

Transcripts and Genome-Loci which were Tested in Real-Time RT-PCR orPCR:

β-Actine: as transcript and genome locus

GAPDH as transcript and genome locus

β-Tubuline as transcript

DNase I Verdau (Example 10 and 11):

In the examples 10 and 11, the DNase I Verdau was carried out asfollows: The DNase I Verdau was the lysate was carried out prior to thereal-time PCR. For this, 2 μl of the lysates was digested in a 20 μlvolume in a suitable buffer which contained 150 μM CaCl₂, 4 mM MgCl₂ and50 mM Tris pH 8.4, with 2 units (units) DNase I. The reaction wasstopped by adding an EDTA/EGTA solution. Then, 2 μl of the reactionsolution was entered into the real-time PCR to measure the amount of theremaining gDNA.

Lysis Example 1 Lysis of Cells in the Presence of Different Additives

It is demonstrated with this experiment that the lysis of cells can bemade more efficient by the addition of an additive. For this, cells werelysed in a lysis buffer which contained imidazole in a concentration of15 mM in H₂O as additive in a first experiment. In a second experiment,cells were lysed in a lysis buffer B, which contained Nonidet-P40,Polyethylenglycol, EGTA and EDTA in addition to the additive imidazole(15 mM). As a comparative example, cells were lysed in a lysis buffer C,which contained Nonidet-P40, polyethylene glycol. EGTA and EDTA. For thedetermination of the lysis efficiency, the CT value of the respectivecellular transcripts was determined in a comparing real-time RT-PCR. TheCt value is the PCR cycle where the PRC signal is detected for the firsttime, that is, becomes visible. The Delta Ct value is calculated in thisexperiment from the difference of the Ct value after the lysis withoutadditive and the Ct value at the lysis while using the additiveimidazole. A negative Delta Ct value points to an improved lysiscompared to the comparing system without additive. A positive Delta Ctvalue points to a lower efficiency with the lysis compared to thecomparing system without additive.

Execution: 40000 293 cells were incubated in a suitable medium for 3days. In a first experiment, the cells were lysed in a lysis buffer,which contains Nonidet-P40, polyethylene glycol. EGTA and EDTA, but noadditive. In a second experiment, the cells were lysed in a lysisbuffer, which contains Nonidet-P40, polyethylene glycol, EGTA. EDTA and15 mM imidazole as additive. In a third experiment, the cells were lysedin a lysis buffer which contained imidazole dissolved in H₂O.

2 μl of the RNA obtained in this manner was converted with Omniscript®,obtained from the company QIAGEN, Hilden, Germany, into a standardreverse transcriptase reaction. After the completion of this reaction, 2μl of the RT reaction solution was transferred to real-time PCRs for thedetection of a certain transcript.

Result: FIG. 1 shows a diagram in which the respectively determinedDelta Ct values of the individual experiments are compared. Theseresults show that cellular RNA showed Delta Ct values in the presence ofthe respective lysis buffers which contained imidazole as additive,which were about 1.5 to 3.5 Cts lower (that is higher negative values)than with the lysis using the usual lysis buffer without imidazole. Thisshows a distinct improvement degree during the lysis.

Example 2 Lysis of Cells in H₂O Using Different Nitrogenous Compounds asAdditives

In this example, the RNA yield with the lysis in H₂O in the presence andabsence of different additives is compared [lysine (1 mM),2,3-dimethylpyrazine (15 mM), imidazole (15 mM), urea (5 mM), spermidine(1 mM)]. An increased yield of RNA points to a more efficient lysis. Soas to exclude possible secondary effects, the RNAs of the respectivelysates were cleaned after the lysis via RNeasy96®, obtained from thecompany QIAGEN, Hilden, Germany, and quantified by densitometricmeasurement of the concentration at 260 nm.

Execution: 20000 MCF7 cells were incubated in a suitable medium in a 96well multititer culture pod. The cells are lysated in H₂O oralternatively in H₂O which contains different additives. The lysate iscleaned via RNeasy 96 (available from QIAGEN GmbH, Hilden, Germany) andmeasured densitometrically at a wavelength of 260 nm. The yield of RNAwith the lysis with H₂O without additive was normalised to a value of100%.

Result: FIG. 2 shows a diagram in which the RNA yields are comparedusing different additives. It results from these results that better RNAyields are achieved by using the respective additive, which points to amore efficient lysis with the use of the additives.

Example 3 Lysis of Cells Using Lysis Buffers and Different Additives

In this example, the RNA yield in the lysis using lysis buffers in thepresence and absence of different additives is compared. An increasedyield of RNA points to a more efficient lysis. So as to exclude possiblesecondary effects, the RNAs of the respective lysates were cleaned afterthe lysis via Rneasy96, available from the company QIAGEN, Hilden,Germany, and quantified at 260 nm by the densitometric measurement ofthe concentration.

Execution: 20000 MCF7 cells are incubated in a suitable medium in a 96well multititer culture pod. The cells are cleaned either in a lysisbuffer containing Nonidet-P40, polyethylene glycol, EGTA and EDTA, orare alternatively lysed in a lysis buffer which contains, in addition tothe mentioned reagents, an additive [arginine (5 mM),

lysine (1 mM), 2,3-dimethylpyrazine (15 mM), imidazole (15 mM),spermidine (1 mM), pyrimidine (15 mM), guanine (15 mM)]. The lysate iscleaned via RNeasy 96 (QIAGEN GmbH, Hilden, Germany) and subsequentlymeasured densitometrically at a wavelength of 260 nm. The RNA yieldduring the lysis with the lysis buffer without additive was normalisedto a value of 100%.

Result: FIG. 3 shows a diagram in which the RNA yields of the differentexperiments are compared. It can be seen from this diagram that anincreased yield could be achieved with all used additives. Aparticularly high yield increase (about 94%) could be used here duringthe use of guanine as additive.

II. Stabilisation Example 4 Stabilisation of Cellular RNA in CellLysates by Different Additives

Cells were lysed in a lysis buffer with or without additives. So as todetermine the degree of the RNA stabilisation, the CT value of acellular transcript was determined in a comparing real-time RT-PCR. TheCt value is the PCR cycle where the PCR signal is detected for the firsttime, that is, becomes visible. The Delta Ct value is calculated in thisexperiment from the difference of the Ct value of the samples of thelysis with additive and the Ct value of the sample of the lysis withoutadditive. The lower, that is, the higher the amount of the negativeDelta Ct value, the higher is the stabilisation effect which is effectedby the addition of the additive to the lysate.

Execution: 40000 HepG2 cells were incubated in a suitable medium for 3days. In a first experiment, the cells were lysed in a lysis buffer,which contains Nonidet-P40, polyethylene glycol. EGTA and EDTA, but noadditive. In further experiments, the cells were lysed in a lysis bufferwhich contains, in addition to the above-mentioned lysis reagents, as anadditive imidazole (15 mM), proline (15 mM), glutamic acid (15 mM),histidines (15 mM), arginines (5 mM), tyrptophane (15 mM), glycine (15mM), pyrimidine (15 mM), guanine (15 mM), cytosine (30 mM), betaine (100mM), ectoine (200 mM) 2,3-dimethylpyrazine (30 mM), 2-aminothiazole (15mM), indazole (15 mM), benzimidazole (15 mM), urea (5 mM) or ammoniumsulfate (30 mM). 2 μl of the RNA obtained in this manner was convertedwith Omniscript® (QIAGEN, Hilden, Germany) into a standard reversetranscriptase reaction. After the completion of the reversetranscriptase reaction. 2 μl of the RT reaction solution was transferredto a real-time PCRs.

Result: FIG. 4 shows a diagram in which the stabilisation of cellularRNA is clarified by the different additives by means of the delta Ctvalue. It can be seen from the diagram that Delta Ct values in theregion of 0.5-8 Cts are achieved in the presence of differentconcentrations of the additive. This clarifies that the stability of theRNA in a lysis buffer with additive is considerably larger compared tothe use of lysis buffers which had no additive added to them.

Example 5 Stabilisation of Cellular RNA in Cell Lysates in the Presenceof Additives

Cells were lysed in a lysis buffer with or without additives. So as todetermine the degree of the RNA stabilisation, the CT value of acellular transcript was determined in a comparing real-time RT-PCR. TheCt value is the PCR cycle where the PRC signal is detected for the firsttime, that is, becomes visible. The Delta Ct value is calculated in thisexperiment from the difference of the Ct value after the lysis withoutadditive and the Ct value at the lysis while using the additiveimidazole. The lower, that is, the higher the amount of the negativeDelta Ct value, the higher is the stabilisation effect which is effectedby the addition of the additive to the lysate.

Execution: 40000 HeLa-, HUH7 and 29293-Zellen cells were incubated in asuitable medium for 3 days. In a first experiment, the cells were lysedin a lysis buffer, which contains Nonidet-P40, polyethylene glycol, EGTAand EDTA. In further experiments, the cells were . . . in a lysis bufferwhich also contained the additives imidazole, lysine or spermine inaddition to the above-mentioned lysis reaction. 2 μl of the RNA obtainedin this manner was converted with Omniscript®, obtained from the companyQIAGEN, Hilden, Germany, into a standard reverse transcriptase reaction.After the completion of this reaction, 2 μl of the RT reaction solutionwas in real-time PCRs for the detection of a certain transcript.

Result: FIG. 5 shows a diagram in which the Delta Ct values of thedifferent samples were compared. It shows that the samples of thecellular RNA of the different cell cultures showed negative Ct values inthe region of about −2 to −5.5 in the presence of differentconcentrations of the additives in contrast to the samples which wereobtained using the—standard lysis buffer without additives. Thisindicates a considerably improved stability of the RNA in the samplescontaining additives.

Example 6 Stabilisation of Cellular RNA in Cell Lysates in the Presenceof Additives

Cells were lysed in a lysis buffer with or without potentiallystabilising additive. RNA was analysed on a denatured gel for thedetermination of the RAN stabilisation. But, as the RNA is complexedwith cellular substance, this first has to be cleaned via Rneasy®(QIAGEN GmbH, Hilden, Germany), so that an analysis on a denaturing gelbecomes possible. The integrity of the RNA can be determined by means ofthe 185 and 28S rRNA bands.

Execution: 40000 HepG2 cells were incubated in a suitable medium for aperiod of 3 days. The cells were respectively lysed in the followinglysis buffers:

1: column 1: a lysis buffer containing Nonidet-P40, polyethylene glycol(PEG), EGTA and EDTA

2: column 2: as 1, additionally containing further 2 mM EGTA

3: column 3: as 1, additionally containing further 2 mM EDTA

4: column 4: a lysis buffer containing Nonidet-P40, EGTA and EDTA

5: column 5: as 1, additionally 1 mM lysine,

6: column 6: as 1, additionally 0.2 mM spermine and

7. column 7: as 1, additionally 10 mM imidazole.

After the lysis in the mentioned lysis buffers, the RNA obtained in thelysate was cleaned via Rneasy and the degradation was checked on adenaturing gel (Agilent BioAnalyzer).

Result: FIG. 6 shows the result of the gel analysis. The degradation ofcellular RNA in the simple lysis buffer with or without PEG (columns 1and 4) can be clearly seen. The RNA in the presence of the additiveslysine, spermine, or imidazole (columns 5, 6 and 7) did not show anydegradation signs in contrast. An improved, but not sufficientstabilisation was found in the presence of increased concentrations ofthe nuclease inhibitors EGTA or EDTA (columns 2 and 3).

Example 7 Stabilisation of Cellular RNA of Cell Lysates by Additives atRoom Temperature

Cells were lysed in a lysis buffer which contained imidazole. For thepurpose of comparison, cellular RNA was cleaned via Rneasy. The lysateswere not subjected to an additional purification step and thereforestill contained all RNases. By the stabilisation of the RNA effected bymeans of the additive imidazole and possibly further cellular substancescontained in the sample, the degradation of the RNA in the lysatesshould diminish or eliminate, even during incubation at roomtemperature.

So as to determine the RNA stabilisation, the Ct value of a cellulartranscript was determined in a comparing real-time RT-PCR. The Ct valueis the PCR cycle where the PRC signal is detected for the first time,that is, becomes visible. The Delta Ct value is calculated from thedifference Ct-Wert (t=0) in the present example, whereby “t” means time,and the Ct value (t=x). If the measured Delta Ct value stays at a valuearound 0 during the measured time, this indicates a high degree of thestabilisation, as this indicates that no significant degradation of theRNA occurs over the measured period.

Execution: 16000 293 cells were incubated in a suitable medium for aperiod of 3 days. On the one hand, the cells were lysed in a lysisbuffer containing Nonidet-P40, polyethylene glycol, EGTA and EDTA, andimidazole on the other hand, the RNA was prepared via RNeasy® (QIAGEN,Hilden, Germany). The lysates or eluates were incubated at roomtemperature for 2 h maximum. 2 μl of the incubated RNA was convertedwith Omniscript®, (QIAGEN. Hilden, Germany), into a standard reversetranscriptase reaction at different times. After the completion of theRT reaction, 2 μl of the reaction solution was transferred to areal-time PCRs.

Result: FIG. 7 shows a diagram in which is shown the dependence of theDelta Ct values on the incubation time. The Delta Ct value of thesamples, which were measured directly from the lysates, and the Delta CTvalue of the RNAs cleaned by means of RNeasy® (QIAGEN GmbH, Hilden.Germany) stayed approximately on the value 0. This shows that the RNAsof the lysates comprise a comparable stability to the RNA preparationcleaned by RNeasy® (QIAGEN GmbH, Hilden, Germany).

Example 8 Stabilisation of Cellular RNA with Different Cell Numbers

While the nucleic acids which were obtained from samples with small cellnumbers can be stabilised by the cellular substances alone, sampleswhich were obtained from large cell numbers still need additional agentswhich support a stabilisation of nucleic acids by cellular substancespossibly taking place. In experiments, in which samples are used fromcultures with different cell numbers, the stability of RNA after thelysis is to be determined with or without stabilising additive.

Execution: 1024-100000 cells were disseminated in 24 well dishes in asuitable medium and incubated for 3 days. In an experiment, the cellsobtained in such a manner were lysed in a lysis buffer, which containsNonidet-P40, polyethylene eglycol. EGTA and EDTA and imidazole asstabilising additive. By the addition of imidazole, a stabilisationwhich is possibly already present, is to be improved by cellularsubstances. In a further experiment, the cells were lysed in a lysisbuffer, which contained Nonidet-P40, polyethylene eglycol, EGTA andEDTA, but no imidazole. The cellular RNA was cleaned via RNeasy® (QIAGENGmbH, Hilden, Germany) in each one of the experiments described above ascomparison. Respectively 2 μl of the lysates or eluates were convertedwith Omniscript®, (QIAGEN, Hilden, Germany), into a standard reversetranscriptase reaction. After the completion of the RT reaction, 2 μl ofthe reaction solution was transferred to a real-time PCRs.

So as to determine the degree of the RNA stabilisation, the CT value ofa cellular transcript was determined in a comparing real-time RT-PCR.The Ct value is the PCR cycle where the PRC signal is detected for thefirst time, that is, becomes visible. The Delta Ct value is calculatedin the present example from the difference of the CT value with a cellnumber X and the Ct value with the cell number 100000. If a largemeasure of stabilisation is reached, the Delta Ct value increases withdecreasing cell number.

Result: FIG. 8 shows a diagram in which the dependence of the Delta Ctvalue on the cell number for the samples which were cleaned via RNeasy®(QIAGEN GmbH, Hilden, Germany) of samples from lysates with imidazole asadditive, and samples without additive. It is clearly shown for thesamples cleaned via RNeasy® (QIAGEN GmbH, Hilden, Germany), that theDelta Ct value behaves corresponding to the cell number over the entirecell number region, that is, that a higher Delta Ct value is observedwith decreasing cell number. If the cells were lysed with the lysisbuffer which also contained imidazole, such a progress of the Delta Ctvalues corresponding to the cell numbers could only be observed from acell number smaller or equal to 40000. But if the cells were lysed witha lysis buffer without imidazole, Delta Ct values corresponding to thecell number could only be observed under 6400 cells. Above 6400 cells,higher Delta Ct values were measured, which indicates a cleardegradation of the RNA, when more than 6400 were introduced. This showsthat a sufficient stabilisation without additive is possible alone bycellular substances such as proteins under a certain cell number (6400cells here). Additives have to support the stabilisation additionallyabove this cell number.

III. Decrease of Inhibiting Effects Example 9 Detectability of gDNA fromNucleoprotein Complexes

Cells were lysed in a lysis buffer with or without additives. A lysingof cells can lead to the formation of a nucleoprotein complex under thelysis conditions chosen here, so that gDNA can only be detectedinsufficiently in a sample obtained from a lysate. For the determinationof the gDNA, the CT value was determined in a comparing real-timeRT-PCR. The Ct value is the PCR cycle where the PRC signal is detectedfor the first time, that is, becomes visible. The Delta Ct value iscalculated in this experiment from the difference of the Ct value afterthe lysis with additive and the Ct value at the lysis without separationadditive. The lower the Delta Ct value, the better the detectability ofgDNA, and the better gDNA could be separated from the nucleoproteincomplex by the additive.

Execution: HepG2 cells were incubated in a suitable medium for a periodof 3 days. As a comparative example, cells were lysed in a lysis bufferC, which contained Nonidet-P40. polyethylene glycol, EGTA and EDTA.Additionally, cells were lysed in further experiments, which alsocontained, in addition to the above-mentioned reagents, the additivesarginine (1 mM), 2,3-dimethylpyrazine (30 mM), tyrptophane (15 mM),histidine (15 mM), indazole (10 mM) or imidazole (15 mM) in the givenconcentrations.

2 μl of the nucleoprotein complexes containing lysates were respectivelytransferred into a real-time PCRs, to detect gDNA.

Result: FIG. 9 shows a diagram in which the respectively determinedDelta Ct values of the individual experiments are compared. With alladditives, increased negative Delta Ct values were found compared to thesample without additive. It can be concluded therefrom that cellulargDNA can be detected better than the gDNA complexed by nucleoproteinsafter separation from cellular nucleoprotein complexes by theabove-mentioned amines. About 0.3 to 3.5 better Delta Ct values could beachieved. This corresponds to an improvement of the detectability ofgDNA by the separation caused by additive by about the factor 1.2 to 10,depending which additive was used for the decomplexing of the cellularnucleoprotein complexes.

Example 10 Improvement of the Enzymatic Degradation (DNase I) of gDNAfrom Cellular Nucleoprotein Complexes

Cells were lysed in a lysis buffer with or without additives. A lysingof cells can lead to the formation of a nucleoprotein complex under thelysis conditions chosen here for the formation of a nucleoproteincomplex, so that gDNA is only accessible insufficiently for the DNase I.The DNase I Verdau of the gDNA serves as measure of how far the gDNA isseparate from the nucleoprotein complexes. If an additive leads to adecomplexing of the gDNA from the nucleoprotein complexes, the gDNAshould be easier to digest by DNase I. The detection of the gDNA bymeans of a real-time assay served for the determination of the enzymaticdegradation by DNase I. The Ct value is the PCR cycle where the PRCsignal is detected for the first time, that is, becomes visible. TheDelta Ct value is calculated in this experiment from the difference ofthe Ct value in a sample with addition of additive, but without additionof DNase I and the Ct value of a sample, to which was added additive andDNase I. The Delta Ct₂ value is calculated in this experiment from thedifference of the Ct value in a sample without addition of additive andDNase I, and the Ct value of a sample, to which was added DNase I, butno additive. The ΔDelta-Ct value is calculated in this experiment fromthe difference: DeltaCt₁-DeltaCt₂. The lower (high amount of thenegative value) the ΔDelta-Ct value, the better the gDNA can be degradedthrough the DNase I, which is a sign for a better accessibility of thegDNA for the DNase I.

Execution: HepG2-Zellen HepG2 cells were incubated in a suitable mediumfor a period of 3 days. As a comparative example, cells were lysed in alysis buffer C, which contained Nonidet-P40, polyethylene glycol, EGTAand EDTA. On the other hand, the cells were lysed in a lysis bufferwhich contained, in addition to the substances mentioned above, alsorespectively one of the following additives in the respectively givenconcentrations: arginine (1 mM), 2,3-dimethylpyrazine (30 mM),aminothazole (15 mM), indazole (30 mM), benzimidazole (15 mM), imidazole(15 mM), tryptophane (15 mM), histidine (15 mM), proline (5 mM) orammonium sulfate (30 mM). Subsequently, a DNase I Verdau was carried outas described above and respectively 2 of the reaction solution obtainedthus was transferred to real-time PCRs to detect gDNA.

Result: FIG. 10 shows a diagram in which the different Delta Ct valueswere compared for different samples.

All used additives led to ΔDelta-Ct values which were more negativewhich indicated that the cellular gDNA of cellular nucleoproteincomplexes can be degraded by decomplexing by means of theabove-mentioned additives reinforced by the DNase I. Depending on theadditive, 0.3 to 10 cycles of better ΔDelta-Ct values were obtained.This corresponds to an improvement of the enzymatic degradability of thegDNA by DNase I, which is achieved by the addition of the additives withthe factor ˜1.2 to ˜100.

A Ct differences of 2 cycles corresponds for example to a change of theamount of starting material available for the PCR, gDNA in the sample,by the factor 4. In this manner, the factor can be correlated with theimprovement with which the accessibility of the gDNA is improved. Thiscontext is explained by means of idealised hypothetic values which donot emanate from any experiments, in FIGS. 10.a.1 and 10.a.2.

Example 11 Concentration Dependence of the Improvement of the EnzymaticDegradation (DNase I) of gDNA from Cellular Nucleoprotein Complexes

The series of experiments carried out above under example 10 was carriedout in an analogous manner using different concentrations of imidazoleas additive.

Execution: HepG2-Zellen 29 cells were incubated in a suitable medium for3 days. As a comparative example, cells were lysed in a lysis buffer C,which contained Nonidet-P40, polyethylene glycol. EGTA and EDTA.Subsequently, a DNase I Verdau was carried out as described above andrespectively 2 μl of the reaction solution obtained thus was transferredto real-time PCRs to detect gDNA.

Result: FIG. 11 shows the concentration dependency of the ΔDelta-Ct fromthe concentration of the indazole added to the lysate. The enzymaticdegradation of the gDNA by DNase I could be improved by a factor 40 whenadding 20 mM indazole.

Example 12 Better DNase I Verdau of gDNA in gDNA/RNA Mixtures in thePresence of Additives

It is tested, if, in nucleic acid mixtures of RNA and DNA, which werecleaned by silica membranes (Rneasy® (QIAGEN GmbH, Hilden, Germany), ause of additives for the decrease of the inhibition by biomolecules willlead to an improved enzymatic degradation by DNase I. For this, cleanedgDNA and cleaned RNA was received in a lysis buffer with or withoutadditive. The accessibility of the gDNA for the DNase I is determined byan enzymatic degradation by means of DNase I with a subsequentdetermination of the gDNA-content by real-time PCR. IN the real-timePCR, the Ct value is the PCR cycle, where the PRC signal is detected forthe first time, that is, becomes visible. The delta Ct value iscalculated in this experiment from the difference of the Ct value afterthe lysis with additive and the Ct value at the lysis without additive.The lower, that is, the more negative, the delta Ct value, the moreeffective is the enzymatic degradation, which again indicates animproved accessibility of the gDNA for the DNase I.

Execution: RNA was cleaned via Rneasy® (QIAGEN GmbH, Hilden, Germany).gDNA was cleaned via QIAamp® (QIAGEN GmbH, Hilden, Germany). 20 ng ofthe gDNA and 20 ng of the RNA were combined to a sample. An enzymaticdegradation by DNase I

The DNase Verdau of the lysates was carried out in the QuantiTect®Real-time buffer (QIAGEN GmbH, Hilden, Germany), whereby 150 μM (as endconcentration) of CaCl₂ was added. The reactions respectively contained20 ng RNA and 20 ng gDNA, 0.5 U DNase (from the company Ambion, USA),primers, nucleotides, HotstarTaq polymerase und die listed additives.The reaction was stopped by heat activation at the PCR. For thedetermination of the remaining gDNA, a real-time PCR is carried out.

Result: FIG. 12 shows a comparison of the Delta Ct values obtainedrespectively. The diagram shows that gDNA in gDNA/RNA mixtures cleanedin the presence of the used additives is degraded by DNase I in aclearly better manner. 2 to 13 cycles improved Delta Ct values could beshown. This corresponds to an improvement of the degradation of gDNA bythe DNase I by the factor ˜4 to >1000, depending which additive wasused.

Example 13 Decrease of the Inhibiting Effect During the Detection ofgDNA and RNA from Cell Lystaes

Cells were lysed in a lysis buffer with or without distamycine D. Alysis of cells leads to the formation of nucleoprotein complexes, sothat RNA can only be detected insufficiently. For the decomplexing ofthe gDNA or RNA, distamycine D was used, which primarily bindsdouble-strand DNA in the small cavity. For the determination of thegDNA, the CT value was determined in a comparing real-time RT-PCR. TheRNA was determined in a comparing real-time RT-PCR. The Ct value is thePCR cycle where the PRC signal is detected for the first time, that is,becomes visible. The delta Ct value is calculated in this experimentfrom the difference of the Ct value after the lysis with additive andthe Ct value at the lysis without additive. The lower, that is, the morenegative, the delta Ct value, the better is the detectability of gDNA orRNA, and the better could the gDNA or RNA be decomplexed from thenucleoprotein complex by the additive.

Execution: HeLa cells which grow in suspension were incubated in asuitable medium. On the one hand, the cells were lysed in a lysisbuffer, which contained Nonidet-P40, polyethylene glycol, EGTA and EDTA.On the other hand, the cells were lysed in a lysis buffer which alsocontained distamine D in different concentrations as additive inaddition to the above-mentioned substances.

Respectively 2 μl of the lysates obtained respectively thus weretransferred to real-time PCRs or real-time RT-PCRs to detect gDNA orRNA.

Result: FIG. 13 shows a diagram in which the respectively determineddelta Ct values of the individual experiments are compared. It can beseen in the diagram that cellular gDNA and RNA can be detected easierafter the decomplexing of cellular nucleoprotein complexes by distamineD that in the samples without distamine D. The degree of the improvementdepends on the concentration of distamycine. For the gDNA, improvementsof the Ct value of >4 cycles could be achieved even with smallconcentrations of 70 pM. This corresponds to an improvement of thefactor>10.

The Ct value improvements during the detection of the RNA during the useod distamycine as additive are smaller here. This can be attributed thatdistamycine primarily binds DNA. The achieved effect is thereby basedessentially on the decomplexing of protein DNA complexes, into which theRNA is woven and also released. The effect on the detectability of RNAis thereby essentially of the indirect type.

Example 14 Decrease of the Inhibiting Effect on RNA, Normed to theDetectability of DNA

Cells were lysed in a lysis buffer with or without additives. The lysisof cells leads to the formation of nucleoprotein complexes, so that RNAcan only be detected insufficiently. For the detection of the RNA, theCT value was determined in a comparing two-tube real-time RT-PCR. The Ctvalue is the PCR cycle where the PRC signal is detected for the firsttime, that is, becomes visible. The delta Ct value is calculated in thisexperiment from the difference of the Ct value after the lysis withadditive and the Ct value at the lysis without additive. The Ct valuesof the RNA were normalised on the Ct values of the gDNA. A Ct differenceof e.g. 2 cycles corresponds to a change of the accessibility of the RNAby the reverse transcriptase by the factor 4. The factor can bedetermined in this manner, with which the accessibility of the RNA fromnucleoprotein complexes, compared to the accessibility of the gDNA fromnucleoprotein complexes by the respective additive.

Execution: HepG2 cells were incubated in a suitable medium for 3 days.On the one hand, the cells were lysed in a lysis buffer, which containedNonidet-P40, polyethylene glycol, EGTA and EDTA. On the other hand, thecells were lysed in a lysis buffer which contained, in addition to thesubstances mentioned above, also respectively one of the followingadditives in the respectively given concentrations: arginine (1 mM),2,3-dimethylpyrazine (30 mM), aminothazole (15 mM), indazole (30 mM),benzimidazole (15 mM), histidine (10 mM), proline (5 mM), tryptophane 10mM, indazole 30 mM), ammonium sulfate 30 mM or imidazole (15 mM). 2 μlof the lysates obtained in this manner was used in a reversetranscriptase reaction with Omniscript RT® (QIAGEN, Hilden, Germany).After the completion of the RT reaction, 1 μl of the reaction solutionwas respectively transferred to a real-time PCRs, so as to detect thecorresponding cDNA.

Result: FIG. 14 shows a diagram in which the respectively achievedimprovements with the detectability of cellular RNA are compared. Thediagram shows that cellular RNA can be detected easier afterdecomplexing of the cellular nucleoprotein complexes by theabove-mentioned additives than RNA from lysate samples, to which noadditive was added. Improvements with the factor 2-1000 could bemeasured. This shows that a clear decomplexing of the RNA fromnucleoprotein complexes results due to the use of the respectiveadditive.

IV. Masking Example 15 Differential Masking of DNA in Mixtures ofCleaned Genomic DNA and Cleaned RNA

Masked DNA should be more difficult to amplify than RNA. Real-time PCRor RT-PCR of DNA and RNA can show the measure of the differentialmasking of the DNA compared to the RNA, when additives are used for themasking of the gDNA.

The Delta Ct value is defined as the difference of the Ct value ofsamples to which were added additive and the Ct value of samples towhich was not added any additive. A high value showed the masking of theDNA compared to the RNA.

Execution: Human gDNA and RNA was respectively cleaned by means ofQIAamp® (QIAGEN GmbH, Hilden, Germany) or Rneasy® (QIAGEN GmbH, Hilden,Germany) 20 ng of the gDNA and 20 ng of the RNA were combined to asample. Spermine up to an end concentration of 5 or 20 μM was added tosome samples. 2 μl of the rest after centrifugation was transferred intoa real-time PCR or a two tube real-time RT-PCR.

Result: FIG. 15 shows a diagram in which the respectively determineddelta Ct values of the individual experiments are compared. It can beseen in the diagram that both nucleic acids, gDNA and RNA are maskedduring the 20 my spermine, when using 5 μM spermine, gDNA can beselectively masked. With 5 μM spermine, a Delta Ct displacement of 6cycles could be measured, which gives a masking of the gDNA with thefactor of ˜500. In contrast, for the RNA was not found a Delta Ctdisplacement.

Example 16 Masking of RNA in Cell Lysates by Different Additives

Masked RNA should be worse to amplify than gDNA from the samepreparation or the same lysate. Real-time RT-PCR of the masked RNAadjusted to the real-time PCR of gDNA should show the extent of thedifferential masking of the DNA compared to the RNA.

The Delta Ct value is defined as the difference of Ct values of sampleswhich were obtained by lysis with additive and the Ct value of sampleswhich were obtained by lysis without additive in the present experiment.The Delta Ct value was normalised on the Ct values which were achievedby the RNA in the real-time RT-PCR.

A high value showed the masking of the DNA compared to the RNA.

Execution: On the one hand, human gDNA and RNA with adetergent-containing lysis buffer (Nonidet-P40, polyethylene glycol,EGTA and EDTA) was obtained from HepG2 cells. On the other hand, theadditives ammonium sulfate, glycine or ammonium hydrogen phosphate in aconcentration of 30 mM or urea in a concentration of 5 mM for thedifferential masking of gDNA.

The differential masking of the DNA compared to RNA was subsequentlydetermined via real-time PCR and real-time RT-PCR.

Result: FIG. 16 shows a diagram in which the respectively determineddelta Ct values of the individual experiments are compared. It can beseen in the diagram that genome DNA in lysis buffer with the mentionedadditives leads to higher Delta Ct values normalised on the Ct values ofthe RNA. This shows a masking of the DNA compared to the RNA. In thecase of the indazole, a masking of nearly 7 Cts was achieved, whichindicates that about 100× less RNA was detected in this solution due tothe masking.

Example 17 Masking of Genomic DNA in Cell Lysates by Different Additives

Masked DNA should be worse to amplify than RNA from the samepreparation. Real-time RT-PCR of the masked RNA adjusted to thereal-time PCR of gDNA should show the extent of the differential maskingof the DNA compared to the RNA.

In this experiment, the delta Ct value is defined as the difference ofthe Ct value (DNA) and Ct-Wert (RNA). A negative delta CT value showedthe masking of the RNA compared to the DNA.

Execution: On the one hand, human gDNA and RNA with adetergent-containing lysis buffer (Nonidet-P40, polyethylene glycol.EGTA and EDTA) was obtained from 40,000 cells. On the other hand, one ofthe following additives were respectively added in the givenconcentrations, so as to mask RNA differentially: glutamic acid (15 mM),arginine (5 mM), 2,3-dimethylpyrazine (15 mM), benzimidazole (15 mM),imidazole (15 mM) or histidine (15 mM). The concentrations arerespectively end concentrations. The differential masking of the DNAcompared to RNA was subsequently determined via real-time PCR andreal-time RT-PCR.

Result: FIG. 17 shows the Delta Ct values obtained respectively. It canbe seen from the diagram that RNA in the lysis buffers containingadditive resulted in negative delta Ct values. This shows a masking ofthe DNA compared to the RNA. In the case of the glutamic acid andarginine, 2,3-dimethylpyrazine and imidazole, a masking of 4 Cts wasachieved, which indicated that about 10× less DNA was detected in thissolution due to the masking.

Example 18 Concentration Dependence of the Masking of Genomic DNA inCell Lysates

Masked DNA should be worse to amplify than RNA from the samepreparation. Real-time RT-PCR of the masked RNA adjusted to thereal-time PCR of gDNA should show the extent of the differential maskingof the DNA compared to the RNA.

In this experiment, the Delta Ct value is defined as the difference ofthe Ct value (RNA) and the Ct value (gDNA). A negative Delta CT valueshowed the masking of the RNA compared to the DNA.

Execution: On the one hand, human gDNA and RNA with adetergent-containing lysis buffer (Nonidet-P40, polyethylene glycol,EGTA and EDTA) was obtained from HepG2 cells. On the other hand, theadditive arginine was respectively added to the lysis buffer indifferent concentrations to achieve a differential masking. The shownconcentrations are respectively end concentrations of the arginine inthe lysate. The differential masking of the DNA compared to RNA wassubsequently determined via real-time PCR and real-time RT-PCR.

Result: FIG. 18 shows a diagram in which the respectively determinedDelta Ct values of the individual experiments are compared. It can beseen from the diagram The Delta Ct values are more negative, the higherthe end concentration of arginine in the buffer. This shows a masking ofthe DNA compared to the RNA. In this experiment series at 6 mM arginie,a maximum masking was obtained. A Delta Ct value of “−6” corresponds toan approximately 500 times worse detection of the gDNA.

Example 19 Masking of RNA in Cell Lysates by Different Additives

Masked RNA should be worse to amplify than gDNA from the samepreparation or the same lysate. Two-tube real-time RT-PCR of the maskedRNA adjusted to the real-time PCR of gDNA should show the extent of thedifferential masking of the RNA compared to the DNA. In this experiment,the Delta Ct value is defined as the difference of the Ct value (DNA)and Ct-Wert (RNA). A negative Delta CT value showed the masking of theRNA compared to the DNA.

Execution: On the one hand, human gDNA and RNA with adetergent-containing lysis buffer (Nonidet-P40, polyethylene glycol,EGTA and EDTA) was obtained from HepG2 cells. On the other hand, one ofthe following additives were respectively added in the givenconcentrations, so as to mask RNA differentially: proline (20 mM),indazole (20 mM) or ammonium sulfate (30 mM). The concentrations arerespectively end concentrations. The RNA was subsequently employed in a20 μl reverse transcriptase using the lysate. 2 μl of the reactionsolution obtained thus was then transferred into the real-time PCR. As acomparison, a real-time PCR was carried out without a priortranscriptase reaction.

Result: FIG. 19 shows a diagram in which the respectively determinedDelta Ct values of the individual experiments are compared. It can beseen from the diagram that RNA in the lysis buffers containing additiveresulted in negative Delta Ct values. This shows a masking of the RNAcompared to the gDNA. In the case of the indazole, a masking of nearly 6Cts was achieved, which indicates that about 400× less RNA was detectedin this solution due to the masking.

Example 20 Use of the Substances According to the Invention for TreatingBiological Samples or Organisms and Measurement of the pH Values

Execution: On the one hand, human gDNA and RNA with adetergent-containing lysis buffer was obtained from HepG2 cells.Alternatively, a) arginine (5 mM) b) arginine and proline (concentrationeach 5 mM) c) imidazole (15 mM) or d) guanosine (20 mM) was added tothis lysis buffer. After the addition of the solution to the cells, thepH value of the lysate obtained in this manner was determined.

Result: The pH values were determined as follows:

sample treated with arginine-containing solution: pH 7.5 to 8

sample treated with arginine-proline-containing solution: pH 7.4 to 8

sample treated with imidazole-containing solution: pH 7.5 to 8

sample treated with guanosine-containing solution: pH>9

1. A method for selective masking of at least one species of a nucleicacid in a sample, wherein said sample comprises at least one firstspecies of a nucleic acid and at least one second species of nucleicacid different from the first species, the method comprising: A)providing said sample which contains at least two different species ofnucleic acid, B) contacting the sample with a fluid and/or solidcomposition to produce a sample preparation, wherein said compositioncomprises at least one nitrogenous compound selected from the groupconsisting of spermidine, ammonium sulfate, ammonium hydrogenphosphate,glycine, 2,3-dimethylpyrazine, benzimidazole, imidazole, arginine,histidine, urea, and distamycine; whereby the producing of said samplepreparation is carried out such that said sample comprising at least onefirst and at least one second species of nucleic acid is mixed with,and/or dissolved and/or suspended in said composition to form saidsample preparation, and wherein the ratio of the concentration of saidfirst species of nucleic acid to the concentration of said secondspecies of nucleic acid in said sample is the same as the ratio ofconcentration of said first species of nucleic acid to the concentrationof said second species of nucleic acid in said sample preparation,whereby the amount of the nitrogenous compound is chosen so that thesecond species of nucleic acid is masked in such a manner that the firstspecies of nucleic acid can be more readily detectable in a detectionmethod for nucleic acids, compared to the same detection method in whichsaid nitrogenous compound is not present.
 2. A method according to claim1, wherein the sample comprises DNA and/or RNA and a protein.
 3. Amethod according to claim 1, wherein the sample comprises DNA and/or RNAand a protein and wherein if lysis is conducted, none of said DNA and/orRNA or said protein is removed before or during said lysis.
 4. A methodaccording to claim 1, wherein said contacting of the sample with a fluidand/or solid composition to produce a sample preparation furthercomprises conducting a lysis.
 5. A method according to claim 1, whereinsaid contacting the sample with a fluid and/or solid composition toproduce a sample preparation further comprises a lysis performed in thepresence of at least one further lysis reagent selected from the groupconsisting of complexing agents, detergents, substances for volumerestriction and solvents.
 6. A method according to claim 1, furthercomprising conducting a detection method for nucleic acids.
 7. A methodaccording to claim 6, wherein said detection method for nucleic acids isselected from the group consisting of nucleic acid binding reactions,nucleic acid hybridisations, Northern and/or Southern blotting,hybridisation of oligo nucleotides and probes, enzymatic modificationsor polymerisations of nucleic acids, sequencing reactions, in-vitrotranscription, restriction endonuclease splittings, amplificationreactions, PCR (polymerase chain reaction), real-time PCR, RT-PCR(reverse transcription polymerase chain reaction), real-time-RT-PCR,NASBA (nucleic acid sequence based amplification), 3SR (sequencesustained self replication), 2 SR, TMA (transcription mediatedamplification), MDA (multiple displacement amplification) rolling circleamplification and rolling transcription amplification.
 8. A methodaccording to claim 6, wherein said detection method for nucleic acids isperformed without any further purification step between step B) and saiddetection method.
 9. A method for sample preparation comprising: A)providing a sample which comprises at least two species of nucleic acidand at least one species of protein, B) lysis of the sample in thepresence of a fluid sample preparation to form a lysate, whereby thefluid sample preparation comprises a pH of about 7.1 to about 14 andwherein the fluid preparation comprises at least one nitrogenouscompound, and wherein the amount of nitrogenous compound is chosen so asto minimize precipitation of nucleic acid and/or protein during lysis orin said lysate produced and further wherein the ratio of concentrationof the at least two species of nucleic acid and protein in the lysateproduced is the same as the ratio of concentration of the at least twospecies of nucleic acid and protein in the sample prior to said lysis,and wherein said nitrogenous compound is capable of masking a firstspecies of nucleic acid in the lysate so that said first species ofnucleic acid has no adverse effects on a subsequent analysis and/orverification procedure of a second different species of nucleic acidcontained in the lysate.
 10. The method of claim 1 wherein contactingthe sample with a fluid and/or solid composition produces a fluid samplepreparation.